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Old JM, Vallin BL, Thorley RK, Casey F, Stannard HJ. DNA metabarcoding analysis of the bare-nosed wombat ( Vombatus ursinus) diet. Ecol Evol 2024; 14:e11432. [PMID: 38770127 PMCID: PMC11103767 DOI: 10.1002/ece3.11432] [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: 11/24/2023] [Revised: 04/29/2024] [Accepted: 05/02/2024] [Indexed: 05/22/2024] Open
Abstract
Wombats are native herbivorous grazers that have adapted to Australia's low-quality forage. Studies on diet selection by bare-nosed wombats (Vombatus ursinus) are limited and are either observational or based on microhistological studies. The current study determined the diet of wombats through DNA metabarcoding across five study sites in New South Wales over a one-year period. Metabarcoding was chosen as it is non-invasive, less time consuming and more specific than traditional techniques. The list of 209 plant species identified as eaten by wombats in this study is much higher than previously reported, with grasses being the most common plant group identified in all samples. Most dietary items identified were introduced plant species. Seasonal differences in plants eaten occurred at four of the five study sites and may reflect dietary abundance and floristic composition at different times of year. Further studies are required to determine if the dietary items differ markedly across the entire range of wombats, and if nutrition influences dietary preferences.
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Affiliation(s)
- Julie M. Old
- School of Science, HawkesburyWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Blaire L. Vallin
- School of Science, HawkesburyWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Rowan K. Thorley
- School of Science, HawkesburyWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Fiona Casey
- School of Science, HawkesburyWestern Sydney UniversityPenrithNew South WalesAustralia
| | - Hayley J. Stannard
- School of Agricultural, Environmental and Veterinary SciencesWagga Wagga, Charles Sturt UniversityWagga WaggaNew South WalesAustralia
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2
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White CQ, Bush JP, Sacks BN. Deer dietary responses to wildfire: Optimal foraging, individual specialization, or opportunism? Mol Ecol 2023; 32:6953-6968. [PMID: 37905672 DOI: 10.1111/mec.17185] [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: 04/17/2023] [Revised: 09/29/2023] [Accepted: 10/17/2023] [Indexed: 11/02/2023]
Abstract
Increasing impacts of wildfire on arid regions of the world fuelled by climate change highlight the need to better understand how natural communities respond to fire. We took advantage of a large (1660-km2 ) wildfire that erupted in northern California during an in-progress study of black-tailed deer (Odocoileus hemionus columbianus) to investigate deer use of and diets within burned and unburned habitats before and after the fire. We compared deer diet breadth to predictions of optimal foraging theory, the niche variation hypothesis, and opportunistic (i.e., generalist) foraging expectations under the assumption that overall availability and diversity of forage in burned areas declined immediately after the fire and increased as the plant community recovered in the next 3 years after the fire. We used faecal pellet counts to document space use and metabarcoding to study diet during pre-fire, post-fire, and recovery periods. Pellet counts supported predictions that deer increased use of unburned sites and reduced use of burn sites after the fire and began to return to burned sites in subsequent sampling years. Diet diversity did not differ significantly between control and burn sites before the fire, but was lower in burn than control sites post-fire (p < .001), when and where diet was dominated by oak (Quercus spp). In contrast, during subsequent years, diet diversity was higher (including more herbaceous plants) in burn than control sites (p < .05). In contrast to predictions of optimal foraging and niche variation hypotheses, individual deer foraged as generalists for which changes in dietary niche breadth paralleled fire-induced changes in diversity of the plant community.
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Affiliation(s)
- Carly Q White
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
| | - Joshua P Bush
- California Department of Fish and Wildlife, Rancho Cordova, California, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit of the Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, California, USA
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3
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Hassan S, Sabreena, Ganiee SA, Yaseen A, Zaman M, Shah AJ, Ganai BA. Unraveling the potential of environmental DNA for deciphering recent advances in plant-animal interactions: a systematic review. PLANTA 2023; 258:117. [PMID: 37957258 DOI: 10.1007/s00425-023-04267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]
Abstract
MAIN CONCLUSION Environmental DNA-based monitoring provides critical insights for enhancing our understanding of plant-animal interactions in the context of worldwide biodiversity decrease for developing a global framework for effective plant biodiversity conservation. To understand the ecology and evolutionary patterns of plant-animal interactions (PAI) and their pivotal roles in ecosystem functioning advances in molecular ecology tools such as Environmental DNA (eDNA) provide unprecedented research avenues. These methods being non-destructive in comparison to traditional biodiversity monitoring methods, enhance the discernment of ecosystem health, integrity, and complex interactions. This review intends to offer a systematic and critical appraisal of the prospective of eDNA for investigating PAI. The review thoroughly discusses and analyzes the recent reports (2015-2022) employing preferred reporting items for systematic reviews and meta-analyses (PRISMA) to outline the recent progression in eDNA approaches for elucidating PAI. The current review envisages that eDNA has a significant potential to monitor both plants and associated cohort of prospective pollinators (avian species and flowering plants, bees and plants, arthropods and plants, bats and plants, etc.). Furthermore, a brief description of the factors that influence the utility and interpretation of PAI eDNA is also presented. The review establishes that factors such as biotic and abiotic, primer selection and taxonomic resolution, and indeterminate spatio-temporal scales impact the availability and longevity of eDNA. The study also identified the limitations that influence PAI detection and suggested possible solutions for better execution of these molecular approaches. Overcoming these research caveats will augment the assortment of PAI analysis through eDNA that could be vital for ecosystem health and integrity. This review forms a critical guide and offers prominent insights for ecologists, environmental managers and researchers to assess and evaluate plant-animal interaction through environmental DNA.
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Affiliation(s)
- Shahnawaz Hassan
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India.
| | - Sabreena
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Shahid Ahmad Ganiee
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Aarif Yaseen
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Muzafar Zaman
- Department of Environmental Science, University of Kashmir, Srinagar, 190006, India
| | - Abdul Jalil Shah
- Department of Pharmaceutical Sciences, University of Kashmir, Srinagar, 190006, India
| | - Bashir Ahmad Ganai
- Centre of Research for Development, University of Kashmir, Srinagar, 190006, India.
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4
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Holthuijzen WA, Flint EN, Green SJ, Plissner JH, Simberloff D, Sweeney D, Wolf CA, Jones HP. An invasive appetite: Combining molecular and stable isotope analyses to reveal the diet of introduced house mice (Mus musculus) on a small, subtropical island. PLoS One 2023; 18:e0293092. [PMID: 37856477 PMCID: PMC10586637 DOI: 10.1371/journal.pone.0293092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
House mice (Mus musculus) pose a conservation threat on islands, where they adversely affect native species' distributions, densities, and persistence. On Sand Island of Kuaihelani, mice recently began to depredate nesting adult mōlī (Laysan Albatross, Phoebastria immutabilis). Efforts are underway to eradicate mice from Sand Island, but knowledge of mouse diet is needed to predict ecosystem response and recovery following mouse removal. We used next-generation sequencing to identify what mice eat on Sand Island, followed by stable isotope analysis to estimate the proportions contributed by taxa to mouse diet. We collected paired fecal and hair samples from 318 mice between April 2018 to May 2019; mice were trapped approximately every eight weeks among four distinct habitat types to provide insight into temporal and spatial variation. Sand Island's mice mainly consume arthropods, with nearly equal (but substantially smaller) contributions of C3 plants, C4 plants, and mōlī. Although seabird tissue is a small portion of mouse diet, mice consume many detrital-feeding arthropods in and around seabird carcasses, such as isopods, flesh flies, ants, and cockroaches. Additionally, most arthropods and plants eaten by mice are non-native. Mouse diet composition differs among habitat types but changes minimally throughout the year, indicating that mice are not necessarily limited by food source availability or accessibility. Eradication of house mice may benefit seabirds on Sand Island (by removing a terrestrial, non-native predator), but it is unclear how arthropod and plant communities may respond and change. Non-native and invasive arthropods and plants previously consumed (and possibly suppressed) by mice may be released post-eradication, which could prevent recovery of native taxa. Comprehensive knowledge of target species' diet is a critical component of eradication planning. Dietary information should be used both to identify and to monitor which taxa may respond most strongly to invasive species removal and to assess if proactive, pre-eradication management activities are warranted.
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Affiliation(s)
- Wieteke A. Holthuijzen
- Department of Ecology & Evolutionary Biology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States of America
| | - Elizabeth N. Flint
- Marine National Monuments of the Pacific, U.S. Fish and Wildlife Service, Honolulu, Hawaiʻi, United States of America
| | - Stefan J. Green
- Genomics and Microbiome Core Facility, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Jonathan H. Plissner
- Midway Atoll National Wildlife Refuge, U.S. Fish and Wildlife Service, Waipahu, Hawaiʻi, United States of America
| | - Daniel Simberloff
- Department of Ecology & Evolutionary Biology, University of Tennessee at Knoxville, Knoxville, Tennessee, United States of America
| | - Dagmar Sweeney
- Institute for Health Research & Policy, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Coral A. Wolf
- Island Conservation, Santa Cruz, California, United States of America
| | - Holly P. Jones
- Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America
- Institute for the Study of the Environment, Sustainability, and Energy, Northern Illinois University, DeKalb, Illinois, United States of America
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5
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Vandergast AG, Brehme CS, Iwanowicz D, Cornman RS, Adsit‐Morris D, Fisher RN. Fecal metabarcoding of the endangered Pacific pocket mouse ( Perognathus longimembris pacificus) reveals a diverse and forb rich diet that reflects local habitat availability. Ecol Evol 2023; 13:e10460. [PMID: 37745784 PMCID: PMC10514273 DOI: 10.1002/ece3.10460] [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: 05/11/2023] [Revised: 08/02/2023] [Accepted: 08/17/2023] [Indexed: 09/26/2023] Open
Abstract
Information on diet breadth and preference can assist in understanding links between food resources and population growth and inform habitat restoration for rare herbivores. We assessed the diet of the endangered Pacific pocket mouse using metabarcoding of fecal samples and compared it to plant community composition in long-term study plots in two populations on Marine Corps Base Camp Pendleton, San Diego County, CA. Fecal samples (n = 221) were collected between spring 2016 and fall 2017 during monthly live-trap surveys. Concurrently, percent cover and plant phenology were measured in plots centered on trap locations. Fecal samples were sequenced with paired-end reads of the internal transcribed spacer 2 region of the nuclear ribosomal gene, and the resulting amplicons were matched to a regionally specific database. Seventy-three plant taxa were detected, which were mostly forbs and perennial herbs (70-90%). Diet composition differed between populations, years, seasons, and plots. Overall, diet and local habitat composition in plots were significantly correlated. However, we detected some differences in above-ground seed availability and proportion in fecal samples that indicate diet preferences for some forbs, perennial herbs, and native bunch grasses over perennial shrubs and non-native grasses. This is the first study of PPM to pair plant phenology surveys with diet metabarcoding to estimate resource selection, and results suggest that managing habitat for diverse native forb communities and reducing non-native grass cover may be beneficial for this critically endangered species.
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Affiliation(s)
- Amy G. Vandergast
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Cheryl S. Brehme
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Deborah Iwanowicz
- U.S. Geological Survey, Eastern Ecological Science Center, Leetown Research LaboratoryKearneysvilleWest VirginiaUSA
| | - Robert S. Cornman
- U.S. Geological SurveyFort Collins Science CenterFort CollinsColoradoUSA
| | - Devin Adsit‐Morris
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
| | - Robert N. Fisher
- U.S. Geological SurveyWestern Ecological Research CenterSan DiegoCaliforniaUSA
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6
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Chen Q, Liu M, Xu C, Bai J, Feng H, Chen C, Zhao L, Liu Y, Zhou S, Zhao D. Potential of plant DNA information in determining the provenance and identify of unknown victims. Forensic Sci Int 2023; 350:111786. [PMID: 37481907 DOI: 10.1016/j.forsciint.2023.111786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 05/29/2023] [Accepted: 07/15/2023] [Indexed: 07/25/2023]
Abstract
Determination of the personal identity of victims is particularly important for the settlement of criminal cases. Unfortunately, useful information for identification is not always available. We here propose that the particles (pollens) of some plants with specific geographical distributions extracted from human lung tissues contribute to further determining the provenance or long-term residence of unknown victims, thereby considerably narrowing the search scope of the victims. We collected lung tissues from 155 victims with diverse causes of death, extracted DNA from lung tissues, sequenced the DNA fragments of plants on the Illumina Hiseq platform, and barcoded the plant species using phylogenetic methods. Finally, 108 unique plant sequences were detected in 55 samples and identified to belong to 36 species in 32 genera of 29 families. These plants were predominantly insect-pollinated crops and ornamental plants. No significant difference was observed between male and female samples, between urban and rural samples, or among samples of different ages and different sample sizes. There were 16 samples with 21 wild plant species. The original sources of 15 samples were overlapped with the distribution regions of detected plants; 2 samples narrowed the original sources to 2 provinces, which were quite coincident with their source places; 1 sample had no overlapping with its victim source region. Although plant information was only found in one-third of the samples, we further demonstrated the great potential of plant eDNA in identifying the source of unnamed corpses in a real-world case. We used plant eDNA from lung tissues to explore the provenance of an unknown female corpse found in Beijing. The source place of this victim was narrowed to Guangdong and Guangxi provinces, and finally, we confirmed her true identity in the list of missing persons in Guangxi Province. In the presence of a well-covered local reference library, the plant species detected in the lungs can be accurately identified. In difficult criminal cases where physical evidence is relatively weak, plant DNA information may provide new clues. In conclusion, the plant particles trapped in the lungs are promising to help forensic experts narrow the search scope for the identity of unknown victims.
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Affiliation(s)
- Qing Chen
- China University of Political Science and Law, Beijing 100091, China; Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Mengyan Liu
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie Bai
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Hua Feng
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Changcan Chen
- Forensic Science Service of Beijing Public Security Bureau, Beijing 100092, China
| | - Liang Zhao
- ShanXi Medical University, Jinzhong 030001, China
| | - Yanlei Liu
- School of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 056038, China.
| | - Shiliang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Dong Zhao
- Key Laboratory of Evidence Science, CUPL, Ministry of Education, Beijing 100088, China.
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7
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Botha D, du Plessis M, Siebert F, Barnard S. Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions. PLoS One 2023; 18:e0286144. [PMID: 37205700 DOI: 10.1371/journal.pone.0286144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/10/2023] [Indexed: 05/21/2023] Open
Abstract
Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.
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Affiliation(s)
- Danielle Botha
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Mornè du Plessis
- Core Sequencing Facility, National Institute for Communicable Diseases of the National Health Laboratory Service, Sandringham, Johannesburg, South Africa
| | - Frances Siebert
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
| | - Sandra Barnard
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa
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8
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Combrink L, Humphreys IR, Washburn Q, Arnold HK, Stagaman K, Kasschau KD, Jolles AE, Beechler BR, Sharpton TJ. Best practice for wildlife gut microbiome research: A comprehensive review of methodology for 16S rRNA gene investigations. Front Microbiol 2023; 14:1092216. [PMID: 36910202 PMCID: PMC9992432 DOI: 10.3389/fmicb.2023.1092216] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 01/18/2023] [Indexed: 02/24/2023] Open
Abstract
Extensive research in well-studied animal models underscores the importance of commensal gastrointestinal (gut) microbes to animal physiology. Gut microbes have been shown to impact dietary digestion, mediate infection, and even modify behavior and cognition. Given the large physiological and pathophysiological contribution microbes provide their host, it is reasonable to assume that the vertebrate gut microbiome may also impact the fitness, health and ecology of wildlife. In accordance with this expectation, an increasing number of investigations have considered the role of the gut microbiome in wildlife ecology, health, and conservation. To help promote the development of this nascent field, we need to dissolve the technical barriers prohibitive to performing wildlife microbiome research. The present review discusses the 16S rRNA gene microbiome research landscape, clarifying best practices in microbiome data generation and analysis, with particular emphasis on unique situations that arise during wildlife investigations. Special consideration is given to topics relevant for microbiome wildlife research from sample collection to molecular techniques for data generation, to data analysis strategies. Our hope is that this article not only calls for greater integration of microbiome analyses into wildlife ecology and health studies but provides researchers with the technical framework needed to successfully conduct such investigations.
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Affiliation(s)
- Leigh Combrink
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,School of Natural Resources and the Environment, University of Arizona, Tucson, AZ, United States
| | - Ian R Humphreys
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Quinn Washburn
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Holly K Arnold
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Keaton Stagaman
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Kristin D Kasschau
- Department of Microbiology, Oregon State University, Corvallis, OR, United States
| | - Anna E Jolles
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States.,Department of Integrative Biology, Oregon State University, Corvallis, OR, United States
| | - Brianna R Beechler
- Department of Biomedical Sciences, Carlson College of Veterinary Medicine, Oregon State University, Corvallis, OR, United States
| | - Thomas J Sharpton
- Department of Microbiology, Oregon State University, Corvallis, OR, United States.,Department of Statistics, Oregon State University, Corvallis, OR, United States
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9
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Lee SK, Woo C, Lee EJ, Yamamoto N. Using high-throughput sequencing to investigate the dietary composition of the Korean water deer (Hydropotes inermis argyropus): a spatiotemporal comparison. Sci Rep 2022; 12:22271. [PMID: 36564425 PMCID: PMC9789119 DOI: 10.1038/s41598-022-26862-z] [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: 03/28/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
The Korean water deer (Hydropotes inermis argyropus) is considered a vermin in Korea because it damages crops, but also listed as a vulnerable species on the IUCN's red list. Therefore, it is indispensable to manage them appropriately by understanding the ecology such as food habits. Here, we aimed to apply high-throughput sequencing (HTS), a sensitive and objective method, to investigate the dietary composition of the Korean water deer inhabiting the lowland and forest areas in summer and winter. We targeted the internal transcribed spacer 2 (ITS2) region for plant identification. From a total of 40 fecal samples analyzed, 63 plant genera were identified, with Morus being the most abundant, and some of the plant taxa identified by HTS were detected for the first time as the diets of Korean water deer. By type, woody plants (68.6%) were the most predominant, followed by forbs (7.0%) and graminoids (0.7%). We found that the deer in the forest area ate more woody plants (84.6%) than those in the lowland area (52.7%). It was also found that the type of woody plants that the deer ate changed by season. Overall, our results indicate that the Korean water deer is a browser that is seasonally adaptable and feeds on a wide variety of woody plants. We expect that the results and genetics methods reported here, by parallelly investigating their habitat range and reproductive behavior in the future, will help the management and conservation of the Korean water deer, which is in contradictory situations.
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Affiliation(s)
- Seung-Kyung Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Cheolwoon Woo
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea
| | - Eun Ju Lee
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, South Korea
| | - Naomichi Yamamoto
- grid.31501.360000 0004 0470 5905Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826 South Korea ,grid.31501.360000 0004 0470 5905Institute of Health and Environment, Seoul National University, Seoul, South Korea
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10
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Chock RY, Miller WB, King SN, Brehme CS, Fisher RN, Sin H, Wilcox P, Terp J, Tremor S, Major MR, Merrill K, Spencer WD, Sullivan S, Shier DM. Quantitative SWOT analysis: A structured and collaborative approach to reintroduction site selection for the endangered Pacific pocket mouse. J Nat Conserv 2022. [DOI: 10.1016/j.jnc.2022.126268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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11
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Correlation and Influence of Seasonal Variation of Diet with Gut Microbiota Diversity and Metabolism Profile of Chipmunk. Animals (Basel) 2022; 12:ani12192586. [PMID: 36230327 PMCID: PMC9559678 DOI: 10.3390/ani12192586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
Tamias Sibiricus is the only member of the genus Tamias, a significant and vigorous seed distributor and vital food for their predators. No information is known about the strict diet, gut microbiota structure, and metabolism profile of chipmunks and how they diversify seasonally. The above factors, as well as flexibility toward seasonal shifts, are critical in defining its growth rates, health, survivorship, and population stability. This study explored the diet, gut microbiota composition, and chipmunk metabolism. Additionally, the influence of different seasons was also investigated by using next-generation sequencing. Results revealed that seasons strongly affected a diet: streptophyte accounted for 37% in spring, which was lower than in summer (34.3%) and autumn (31.4%). Further, Ascomycota was observed at 43.8% in spring, which reduced to 36.6% in summer and the lowest (31.3%) in autumn. Whereas, nematodes showed maximum abundance from spring (15.8%) to summer (20.6%) and autumn (24.1%). These results signify the insectivorous nature of the chipmunk in summer and autumn. While herbivorous and fungivorous nature in spring. The DNA analysis revealed that chipmunk mainly feeds on fungi, including Aspergillus and Penicillium genus. Similar to diet composition, the microbiome also exhibited highly significant dissimilarity (p < 0.001, R = 0.235) between spring/autumn and spring/summer seasons. Proteobacteria (35.45%), Firmicutes (26.7%), and Bacteroidetes (23.59%) were shown to be the better discriminators as they contributed the most to causing differences between seasons. Moreover, PICRUSt showed that the assimilation of nutrients were also varied seasonally. The abundance of carbohydrates, lipids, nucleotides, xenobiotics, energy, terpenoids, and polyketides metabolism was higher in spring than in other seasons. Our study illustrates that seasonal reconstruction in the chipmunk diet has a significant role in shaping temporal variations in gut microbial community structure and metabolism profile.
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12
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Aylward CM, Statham MJ, Barthman-Thompson L, Kelt DA, Sacks BN. Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding. Ecol Evol 2022; 12:e9121. [PMID: 35866012 PMCID: PMC9289124 DOI: 10.1002/ece3.9121] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 11/05/2022] Open
Abstract
The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant.
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Affiliation(s)
- Cody M Aylward
- Department of Wildlife, Fish, and Conservation University of California, Davis Davis California USA.,Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine University of California, Davis Davis California USA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine University of California, Davis Davis California USA
| | | | - Douglas A Kelt
- Department of Wildlife, Fish, and Conservation University of California, Davis Davis California USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine University of California, Davis Davis California USA.,Department of Population Health and Reproduction, School of Veterinary Medicine University of California, Davis Davis California USA
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Neby M, Kamenova S, Devineau O, Ims RA, Soininen EM. Issues of under-representation in quantitative DNA metabarcoding weaken the inference about diet of the tundra vole Microtus oeconomus. PeerJ 2021; 9:e11936. [PMID: 34527438 PMCID: PMC8403475 DOI: 10.7717/peerj.11936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022] Open
Abstract
During the last decade, methods based on high-throughput sequencing such as DNA metabarcoding have opened up for a range of new questions in animal dietary studies. One of the major advantages of dietary metabarcoding resides in the potential to infer a quantitative relationship between sequence read proportions and biomass of ingested food. However, this relationship's robustness is highly dependent on the system under study, calling for case-specific assessments. Herbivorous small rodents often play important roles in the ecosystem, and the use of DNA metabarcoding for analyses of rodent diets is increasing. However, there has been no direct validation of the quantitative reliability of DNA metabarcoding for small rodents. Therefore, we used an experimental approach to assess the relationship between input plant biomass and sequence reads proportions from DNA metabarcoding in the tundra vole Microtus oeconomus. We found a weakly positive relationship between the number of high-throughput DNA sequences and the expected biomass proportions of food plants. The weak relationship was possibly caused by a systematic under-amplification of one of the three plant taxa fed. Generally, our results add to the growing evidence that case-specific validation studies are required to reliably make use of sequence read abundance as a proxy of relative food proportions in the diet.
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Affiliation(s)
- Magne Neby
- Department of Applied Ecology, Inland Norway University of Applied Sciences, Koppang, Norway
| | | | - Olivier Devineau
- Department of Applied Ecology, Inland Norway University of Applied Sciences, Koppang, Norway
| | - Rolf A. Ims
- Department of Arctic and Marine Biology, UiT—the Arctic University of Norway, Tromsø, Norway
| | - Eeva M. Soininen
- Department of Arctic and Marine Biology, UiT—the Arctic University of Norway, Tromsø, Norway
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Guo Y, Zhao X, Liu M, Zhang C, Zhang Y, Ma Q, Wang B, Luo H. Using Fecal DNA Metabarcoding to Investigate Foraging Reveals the Effects of Specific Herbage on the Improved n-3 Fatty Acid (PUFA) Composition in the Longissimus Dorsi Muscle of Grazing Tan Sheep. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:9725-9734. [PMID: 34378390 DOI: 10.1021/acs.jafc.1c03788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Understanding the natural diet of grazing sheep can help fulfill their nutritional requirements and positively affect the quality of their meat. Emerging fecal DNA (fDNA) metabarcoding technology can provide more accurate estimates for the dietary composition of free-ranging animals. This study has shown that pasture feeding can promote deposition of n-3 polyunsaturated fatty acids (PUFAs) in Tan lambs' muscle and decrease the ratio of n-6/n-3 fatty acids (FAs), and thus, we investigated the dietary composition of grazing lambs using fDNA metabarcoding to assess the prevalence of medicinal herbage plants in their diet. Herein, based on the full-time natural pasture grazing and 4-h natural pasture grazing with indoor feeding patterns, the herbage taxa (Bassia scoparia, Euphorbia humifusa, Arnebia euchroma, and Salsola sp.) most correlated to n-3 PUFAs were highlighted to elucidate how diversification in dietary components was associated with the muscle FA profile of lambs. Our findings provide experimental evidence for future feeding research.
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Affiliation(s)
- Yanping Guo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xingang Zhao
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Ming Liu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Can Zhang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yingjun Zhang
- Key Laboratory of Grasslands Management and Utilization, College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Qing Ma
- Research Center of Grass and Livestock, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan 750002, Ningxia, China
| | - Bing Wang
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hailing Luo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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Tosa MI, Dziedzic EH, Appel CL, Urbina J, Massey A, Ruprecht J, Eriksson CE, Dolliver JE, Lesmeister DB, Betts MG, Peres CA, Levi T. The Rapid Rise of Next-Generation Natural History. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.698131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Many ecologists have lamented the demise of natural history and have attributed this decline to a misguided view that natural history is outdated and unscientific. Although there is a perception that the focus in ecology and conservation have shifted away from descriptive natural history research and training toward hypothetico-deductive research, we argue that natural history has entered a new phase that we call “next-generation natural history.” This renaissance of natural history is characterized by technological and statistical advances that aid in collecting detailed observations systematically over broad spatial and temporal extents. The technological advances that have increased exponentially in the last decade include electronic sensors such as camera-traps and acoustic recorders, aircraft- and satellite-based remote sensing, animal-borne biologgers, genetics and genomics methods, and community science programs. Advances in statistics and computation have aided in analyzing a growing quantity of observations to reveal patterns in nature. These robust next-generation natural history datasets have transformed the anecdotal perception of natural history observations into systematically collected observations that collectively constitute the foundation for hypothetico-deductive research and can be leveraged and applied to conservation and management. These advances are encouraging scientists to conduct and embrace detailed descriptions of nature that remain a critically important component of the scientific endeavor. Finally, these next-generation natural history observations are engaging scientists and non-scientists alike with new documentations of the wonders of nature. Thus, we celebrate next-generation natural history for encouraging people to experience nature directly.
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Hendier A, Chatelain C, Du Pasquier P, Paris M, Ouattara K, Koné I, Croll D, Zuberbühler K. A new method to determine the diet of pygmy hippopotamus in Taï National Park, Côte d’Ivoire. Afr J Ecol 2021. [DOI: 10.1111/aje.12888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alba Hendier
- Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS) Abidjan Ivory Coast
| | - Cyrille Chatelain
- Conservatoire et Jardin Botaniques de la ville de Genève Geneva Switzerland
| | | | - Monique Paris
- Institute for Breeding Rare and Endangered African Mammals (IBREAM) Edinburgh UK
- Mammal Research Institute Faculty of Natural and Agricultural Sciences University of Pretoria Pretoria South Africa
| | - Karim Ouattara
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS) Abidjan Ivory Coast
- Université Félix Houphouët‐Boigny Abidjan Ivory Coast
| | - Inza Koné
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS) Abidjan Ivory Coast
| | - Daniel Croll
- Institute of Biology University of Neuchâtel Neuchâtel Switzerland
| | - Klaus Zuberbühler
- Institute of Biology University of Neuchâtel Neuchâtel Switzerland
- Centre Suisse de Recherches Scientifiques en Côte d'Ivoire (CSRS) Abidjan Ivory Coast
- School of Psychology and Neuroscience University of St Andrews St Andrews UK
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Cornman RS, McKenna JE, Fike JA. Composition and distribution of fish environmental DNA in an Adirondack watershed. PeerJ 2021; 9:e10539. [PMID: 33680576 PMCID: PMC7919543 DOI: 10.7717/peerj.10539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 11/19/2020] [Indexed: 11/24/2022] Open
Abstract
Background Environmental DNA (eDNA) surveys are appealing options for monitoring aquatic biodiversity. While factors affecting eDNA persistence, capture and amplification have been heavily studied, watershed-scale surveys of fish communities and our confidence in such need further exploration. Methods We characterized fish eDNA compositions using rapid, low-volume filtering with replicate and control samples scaled for a single Illumina MiSeq flow cell, using the mitochondrial 12S ribosomal RNA locus for taxonomic profiling. Our goals were to determine: (1) spatiotemporal variation in eDNA abundance, (2) the filtrate needed to achieve strong sequencing libraries, (3) the taxonomic resolution of 12S ribosomal sequences in the study environment, (4) the portion of the expected fish community detectable by 12S sequencing, (5) biases in species recovery, (6) correlations between eDNA compositions and catch per unit effort (CPUE) and (7) the extent that eDNA profiles reflect major watershed features. Our bioinformatic approach included (1) estimation of sequencing error from unambiguous mappings and simulation of taxonomic assignment error under various mapping criteria; (2) binning of species based on inferred assignment error rather than by taxonomic rank; and (3) visualization of mismatch distributions to facilitate discovery of distinct haplotypes attributed to the same reference. Our approach was implemented within the St. Regis River, NY, USA, which supports tribal and recreational fisheries and has been a target of restoration activities. We used a large record of St. Regis-specific observations to validate our assignments. Results We found that 300 mL drawn through 25-mm cellulose nitrate filters yielded greater than 5 ng/µL DNA at most sites in summer, which was an approximate threshold for generating strong sequencing libraries in our hands. Using inferred sequence error rates, we binned 12S references for 110 species on a state checklist into 85 single-species bins and seven multispecies bins. Of 48 bins observed by capture survey in the St. Regis, we detected eDNA consistent with 40, with an additional four detections flagged as potential contaminants. Sixteen unobserved species detected by eDNA ranged from plausible to implausible based on distributional data, whereas six observed species had no 12S reference sequence. Summed log-ratio compositions of eDNA-detected taxa correlated with log(CPUE) (Pearson’s R = 0.655, P < 0.001). Shifts in eDNA composition of several taxa and a genotypic shift in channel catfish (Ictalurus punctatus) coincided with the Hogansburg Dam, NY, USA. In summary, a simple filtering apparatus operated by field crews without prior expertise gave useful summaries of eDNA composition with minimal evidence of field contamination. 12S sequencing achieved useful taxonomic resolution despite the short marker length, and data exploration with standard bioinformatic tools clarified taxonomic uncertainty and sources of error.
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Affiliation(s)
- Robert S Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
| | - James E McKenna
- U.S. Geological Survey, Great Lakes Science Center, Cortland, NY, USA
| | - Jennifer A Fike
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, CO, USA
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Tuyisenge MF, Eckardt W, Nshutiyayesu S, Devore M. A Simple and Environmentally Friendly Field Method for Fecal Analysis of Herbivore Diet. WILDLIFE SOC B 2020. [DOI: 10.1002/wsb.1143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Marie Fidele Tuyisenge
- Dian Fossey Gorilla Fund International PB 105 Musanze Rwanda
- University of Rwanda PB 117 Butare Rwanda
| | - Winnie Eckardt
- Dian Fossey Gorilla Fund International PB 105 Musanze Rwanda
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19
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Meyer JM, Leempoel K, Losapio G, Hadly EA. Molecular Ecological Network Analyses: An Effective Conservation Tool for the Assessment of Biodiversity, Trophic Interactions, and Community Structure. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.588430] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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Castle ST, Allan N, Clifford D, Aylward CM, Ramsey J, Fascetti AJ, Pesapane R, Roy A, Statham M, Sacks B, Foley J. Diet composition analysis provides new management insights for a highly specialized endangered small mammal. PLoS One 2020; 15:e0240136. [PMID: 33007017 PMCID: PMC7531790 DOI: 10.1371/journal.pone.0240136] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
The critically endangered Amargosa vole (Microtus californicus scirpensis) is found only in rare marsh habitat near Tecopa, California in a plant community dominated by three-square bulrush (Schoenoplectus americanus). Since the earliest research on the Amargosa vole, the existing paradigm has been that these voles are obligatorily dependent on bulrush as their only food source and for the three-dimensional canopy and litter structure it provides for predator avoidance. However, no prior research has confirmed the diet of the Amargosa vole. In this study we characterized the Amargosa vole' nutritional needs, analyzed the quality of bulrush by forage analysis, and performed microhistological and metabarcoding analyses of vole feces to determine what foods were consumed in the wild. All bulrush plant tissues analyzed were low in fat (from 0.9% of dry matter in roots to 3.6% in seeds), high in neutral detergent fiber (from 5.9% in rhizomes to 33.6% in seeds), and low in protein (7.3-8.4%). These findings support the conclusion that bulrush alone is unlikely to support vole survival and reproduction. Fecal microhistology and DNA metabarcoding revealed relatively diverse diets including plants in 14 families, with rushes (Juncaceae), bulrushes (Cyperaceae), and grasses (Poaceae) being the most common diet items. On microhistology, all analyzed samples contained bulrush, sedges (Carex sp.), rushes (Juncus sp.), and beaked spikerush (Eleocharis rostrellata) even from marshes where non-bulrush plants were uncommon. There was evidence of insects at <1% in two marshes but none in the remaining marshes. Metabarcoding detected ten genera of plants. When considering non-Schoenoplectus targets, for which metabarcoding had poor sensitivity, saltgrass (Distichlis spicata) was the most commonly detected species, with prominent contributions from seaside arrowgrass (Triglochin concinna) and yerba mansa (Anemopsis californica) as well. Diversity of vole diets generally increased with increasing site plant diversity, but differences were not statistically significant. Confirming details about dietary behaviors is critical for informing appropriate conservation planning including habitat management and reintroduction of voles into new sites.
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Affiliation(s)
- Stephanie T. Castle
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Nora Allan
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Deana Clifford
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
- Wildlife Investigations Lab, California Department of Fish and Wildlife, Rancho Cordova, CA, United States of America
| | - Cody M. Aylward
- Department of Fish, Wildlife and Conservation Biology, University of California, Davis, CA, United States of America
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Jon Ramsey
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Andrea J. Fascetti
- Department of Molecular Biosciences, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Risa Pesapane
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Austin Roy
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Mark Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
| | - Benjamin Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, United States of America
- Department of Population Health, and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, United States of America
| | - Janet Foley
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, United States of America
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Goldberg AR, Conway CJ, Tank DC, Andrews KR, Gour DS, Waits LP. Diet of a rare herbivore based on DNA metabarcoding of feces: Selection, seasonality, and survival. Ecol Evol 2020; 10:7627-7643. [PMID: 32760553 PMCID: PMC7391308 DOI: 10.1002/ece3.6488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 01/18/2023] Open
Abstract
In herbivores, survival and reproduction are influenced by quality and quantity of forage, and hence, diet and foraging behavior are the foundation of an herbivore's life history strategy. Given the importance of diet to most herbivores, it is imperative that we know the species of plants they prefer, especially for herbivorous species that are at risk for extinction. However, it is often difficult to identify the diet of small herbivores because: (a) They are difficult to observe, (b) collecting stomach contents requires sacrificing animals, and (c) microhistology requires accurately identifying taxa from partially digested plant fragments and likely overemphasizes less-digestible taxa. The northern Idaho ground squirrel (Urocitellus brunneus) is federally threatened in the United States under the Endangered Species Act. We used DNA metabarcoding techniques to identify the diet of 188 squirrels at 11 study sites from fecal samples. We identified 42 families, 126 genera, and 120 species of plants in the squirrel's diet. Our use of three gene regions was beneficial because reliance on only one gene region (e.g., only trnL) would have caused us to miss >30% of the taxa in their diet. Northern Idaho ground squirrel diet differed between spring and summer, frequency of many plants in the diet differed from their frequency within their foraging areas (evidence of selective foraging), and several plant genera in their diet were associated with survival. Our results suggest that while these squirrels are generalists (they consume a wide variety of plant species), they are also selective and do not eat plants relative to availability. Consumption of particular genera such as Perideridia may be associated with higher overwinter survival.
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Affiliation(s)
- Amanda R. Goldberg
- Idaho Cooperative Fish and Wildlife Research UnitDepartment of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Courtney J. Conway
- U.S. Geological SurveyIdaho Cooperative Fish and Wildlife Research UnitUniversity of IdahoMoscowIDUSA
| | - David C. Tank
- Department of Biological Sciences and Stillinger HerbariumUniversity of IdahoMoscowIDUSA
| | - Kimberly R. Andrews
- Department of Fish & Wildlife Sciences and Institute for Bioinformatics and Evolutionary Studies (IBEST)University of IdahoMoscowIDUSA
| | - Digpal S. Gour
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIDUSA
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Camp A, Croxford AE, Ford CS, Baumann U, Clements PR, Hiendleder S, Woolford L, Netzel G, Boardman WSJ, Fletcher MT, Wilkinson MJ. Dual-locus DNA metabarcoding reveals southern hairy-nosed wombats (Lasiorhinus latifrons Owen) have a summer diet dominated by toxic invasive plants. PLoS One 2020; 15:e0229390. [PMID: 32142513 PMCID: PMC7059939 DOI: 10.1371/journal.pone.0229390] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 02/05/2020] [Indexed: 11/23/2022] Open
Abstract
Habitat degradation and summer droughts severely restrict feeding options for the endangered southern hairy-nosed wombat (SHNW; Lasiorhinus latifrons). We reconstructed SHNW summer diets by DNA metabarcoding from feces. We initially validated rbcL and ndhJ diet reconstructions using autopsied and captive animals. Subsequent diet reconstructions of wild wombats broadly reflected vegetative ground cover, implying local rather than long-range foraging. Diets were all dominated by alien invasives. Chemical analysis of alien food revealed Carrichtera annua contains high levels of glucosinolates. Clinical examination (7 animals) and autopsy (12 animals) revealed that the most degraded site also contained most individuals showing signs of glucosinolate poisoning. We infer that dietary poisoning through the ingestion of alien invasives may have contributed to the recent population crashes in the region. In floristically diverse sites, individuals appear to be able to manage glucosinolate intake by avoidance or episodic feeding but this strategy is less tractable in the most degraded sites. We conclude that recovery of the most affected populations may require effective Carrichtera management and interim supplementary feeding. More generally, we argue that protection against population decline by poisoning in territorial herbivores requires knowledge of their diet and of those food plants containing toxic principles.
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Affiliation(s)
- Amanda Camp
- School of Animal and Veterinary Science and Davies Research Centre, The University of Adelaide, Adelaide, SA, Australia
| | - Adam E. Croxford
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | | | - Ute Baumann
- Australian Centre for Plant Functional Genomics, The University of Adelaide, Adelaide, SA, Australia
| | - Peter R. Clements
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
| | - Stefan Hiendleder
- School of Animal and Veterinary Science and Davies Research Centre, The University of Adelaide, Adelaide, SA, Australia
| | - Lucy Woolford
- School of Animal and Veterinary Science and Davies Research Centre, The University of Adelaide, Adelaide, SA, Australia
| | - Gabrielle Netzel
- Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Wayne S. J. Boardman
- School of Animal and Veterinary Science and Davies Research Centre, The University of Adelaide, Adelaide, SA, Australia
| | - Mary T. Fletcher
- Centre for Animal Science, The University of Queensland, Brisbane, Queensland, Australia
| | - Mike J. Wilkinson
- Institute of Biological Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Wales, United Kingdom
- * E-mail:
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Statham MJ, (Smith) Woollett DA, Fresquez S, Pfeiffer J, Richmond J, Whitelaw A, Richards NL, Westphal MF, Sacks BN. Noninvasive Identification of Herpetofauna: Pairing Conservation Dogs and Genetic Analysis. J Wildl Manage 2019. [DOI: 10.1002/jwmg.21772] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Mark J. Statham
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | | | - Susan Fresquez
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
| | - Jerene Pfeiffer
- Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue/Old Davis Road Davis CA 95616‐8744 USA
| | - Jonathan Richmond
- U.S. Geological Survey 4165 Spruance Rd. Suite 200 San Diego CA 92101 USA
| | - Alice Whitelaw
- Working Dogs for Conservation P.O. Box 280 Bozeman MT 59771 USA
| | | | - Michael F. Westphal
- U.S. Bureau of Land Management Central Coast Field Office Marina CA 93933 USA
| | - Benjamin N. Sacks
- Department of Population Health and Reproduction, School of Veterinary Medicine, Mammalian Ecology and Conservation Unit, Veterinary Genetics LaboratoryUniversity of California One Shields Avenue Davis CA 95616‐8744 USA
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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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25
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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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26
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Lamb PD, Hunter E, Pinnegar JK, Creer S, Davies RG, Taylor MI. How quantitative is metabarcoding: A meta-analytical approach. Mol Ecol 2018; 28:420-430. [PMID: 30408260 PMCID: PMC7379500 DOI: 10.1111/mec.14920] [Citation(s) in RCA: 142] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/25/2018] [Accepted: 10/26/2018] [Indexed: 12/12/2022]
Abstract
Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.
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Affiliation(s)
- Philip D Lamb
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Ewan Hunter
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - John K Pinnegar
- School of Environmental Sciences, University of East Anglia, Norwich, UK.,Cefas, Lowestoft, UK
| | - Simon Creer
- School of Biological Sciences, Bangor University, Bangor, UK
| | - Richard G Davies
- School of Biological Sciences, University of East Anglia, Norwich, UK
| | - Martin I Taylor
- School of Biological Sciences, University of East Anglia, Norwich, UK
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27
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Alberdi A, Aizpurua O, Bohmann K, Gopalakrishnan S, Lynggaard C, Nielsen M, Gilbert MTP. Promises and pitfalls of using high‐throughput sequencing for diet analysis. Mol Ecol Resour 2018; 19:327-348. [DOI: 10.1111/1755-0998.12960] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/19/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Antton Alberdi
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Ostaizka Aizpurua
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Kristine Bohmann
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- School of Biological Sciences University of East Anglia Norwich Norfolk UK
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Christina Lynggaard
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Martin Nielsen
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
| | - Marcus Thomas Pius Gilbert
- Section for Evolutionary Genomics, Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark
- NTNU University Museum Trondheim Norway
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28
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Moorhouse-Gann RJ, Dunn JC, de Vere N, Goder M, Cole N, Hipperson H, Symondson WOC. New universal ITS2 primers for high-resolution herbivory analyses using DNA metabarcoding in both tropical and temperate zones. Sci Rep 2018; 8:8542. [PMID: 29867115 PMCID: PMC5986805 DOI: 10.1038/s41598-018-26648-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/15/2018] [Indexed: 11/20/2022] Open
Abstract
DNA metabarcoding is a rapidly growing technique for obtaining detailed dietary information. Current metabarcoding methods for herbivory, using a single locus, can lack taxonomic resolution for some applications. We present novel primers for the second internal transcribed spacer of nuclear ribosomal DNA (ITS2) designed for dietary studies in Mauritius and the UK, which have the potential to give unrivalled taxonomic coverage and resolution from a short-amplicon barcode. In silico testing used three databases of plant ITS2 sequences from UK and Mauritian floras (native and introduced) totalling 6561 sequences from 1790 species across 174 families. Our primers were well-matched in silico to 88% of species, providing taxonomic resolution of 86.1%, 99.4% and 99.9% at the species, genus and family levels, respectively. In vitro, the primers amplified 99% of Mauritian (n = 169) and 100% of UK (n = 33) species, and co-amplified multiple plant species from degraded faecal DNA from reptiles and birds in two case studies. For the ITS2 region, we advocate taxonomic assignment based on best sequence match instead of a clustering approach. With short amplicons of 187-387 bp, these primers are suitable for metabarcoding plant DNA from faecal samples, across a broad geographic range, whilst delivering unparalleled taxonomic resolution.
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Affiliation(s)
- Rosemary J Moorhouse-Gann
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
| | - Jenny C Dunn
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, The Lodge, Potton Road, Sandy, Bedfordshire, SG19 2DL, UK.
- School of Life Sciences, University of Lincoln, Joseph Banks Laboratories, Green Lane, Lincoln, LN6 7TS, UK.
| | - Natasha de Vere
- National Botanic Garden of Wales, Llanarthne, Carmarthenshire, SA32 8HG, UK
- Institute of Biological, Environmental & Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, Ceredigion, SY23 3DA, UK
| | - Martine Goder
- Mauritian Wildlife Foundation, Grannum Road, Vacoas, Mauritius
| | - Nik Cole
- Mauritian Wildlife Foundation, Grannum Road, Vacoas, Mauritius
- Durrell Wildlife Conservation Trust, Les Augrès Manor, La Profonde Rue, Trinity, JE3 5BP Jersey, Channel Islands, UK
| | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - William O C Symondson
- School of Biosciences, Cardiff University, The Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
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29
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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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30
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Galan M, Pons JB, Tournayre O, Pierre É, Leuchtmann M, Pontier D, Charbonnel N. Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Mol Ecol Resour 2018; 18:474-489. [PMID: 29288544 DOI: 10.1111/1755-0998.12749] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/29/2017] [Accepted: 12/23/2017] [Indexed: 12/26/2022]
Abstract
Assessing diet variability is of main importance to better understand the biology of bats and design conservation strategies. Although the advent of metabarcoding has facilitated such analyses, this approach does not come without challenges. Biases may occur throughout the whole experiment, from fieldwork to biostatistics, resulting in the detection of false negatives, false positives or low taxonomic resolution. We detail a rigorous metabarcoding approach based on a short COI minibarcode and two-step PCR protocol enabling the "all at once" taxonomic identification of bats and their arthropod prey for several hundreds of samples. Our study includes faecal pellets collected in France from 357 bats representing 16 species, as well as insect mock communities that mimic bat meals of known composition, negative and positive controls. All samples were analysed using three replicates. We compare the efficiency of DNA extraction methods, and we evaluate the effectiveness of our protocol using identification success, taxonomic resolution, sensitivity and amplification biases. Our parallel identification strategy of predators and prey reduces the risk of mis-assigning prey to wrong predators and decreases the number of molecular steps. Controls and replicates enable to filter the data and limit the risk of false positives, hence guaranteeing high confidence results for both prey occurrence and bat species identification. We validate 551 COI variants from arthropod including 18 orders, 117 family, 282 genus and 290 species. Our method therefore provides a rapid, resolutive and cost-effective screening tool for addressing evolutionary ecological issues or developing "chirosurveillance" and conservation strategies.
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Affiliation(s)
- Maxime Galan
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | - Jean-Baptiste Pons
- LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France
| | - Orianne Tournayre
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | - Éric Pierre
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
| | | | - Dominique Pontier
- LabEx ECOFECT Ecoevolutionary Dynamics of Infectious Diseases, Université de Lyon, Lyon, France.,CNRS, Laboratoire de Biométrie et Biologie Évolutive, UMR5558, Université de Lyon, Université Lyon 1, Villeurbanne, France
| | - Nathalie Charbonnel
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Université de Montpellier, Montferrier sur Lez Cedex, France
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