1
|
Bhendarkar M, Rodriguez-Ezpeleta N. Exploring uncharted territory: new frontiers in environmental DNA for tropical fisheries management. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:617. [PMID: 38874640 DOI: 10.1007/s10661-024-12788-8] [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: 11/07/2023] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
Tropical ecosystems host a significant share of global fish diversity contributing substantially to the global fisheries sector. Yet their sustainable management is challenging due to their complexity, diverse life history traits of tropical fishes, and varied fishing techniques involved. Traditional monitoring techniques are often costly, labour-intensive, and/or difficult to apply in inaccessible sites. These limitations call for the adoption of innovative, sensitive, and cost-effective monitoring solutions, especially in a scenario of climate change. Environmental DNA (eDNA) emerges as a potential game changer for biodiversity monitoring and conservation, especially in aquatic ecosystems. However, its utility in tropical settings remains underexplored, primarily due to a series of challenges, including the need for a comprehensive barcode reference library, an understanding of eDNA behaviour in tropical aquatic environments, standardized procedures, and supportive biomonitoring policies. Despite these challenges, the potential of eDNA for sensitive species detection across varied habitats is evident, and its global use is accelerating in biodiversity conservation efforts. This review takes an in-depth look at the current state and prospects of eDNA-based monitoring in tropical fisheries management research. Additionally, a SWOT analysis is used to underscore the opportunities and threats, with the aim of bridging the knowledge gaps and guiding the more extensive and effective use of eDNA-based monitoring in tropical fisheries management. Although the discussion applies worldwide, some specific experiences and insights from Indian tropical fisheries are shared to illustrate the practical application and challenges of employing eDNA in a tropical context.
Collapse
Affiliation(s)
- Mukesh Bhendarkar
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain.
- ICAR-National Institute of Abiotic Stress Management, Baramati, 413 115, Maharashtra, India.
| | - Naiara Rodriguez-Ezpeleta
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA), 48395, Sukarrieta, Bizkaia, Spain
| |
Collapse
|
2
|
Osman NA, Abdul-Latiff MAB, Mohd-Ridwan AR, Yaakop S, Karuppannan KV, Md-Zain BM. Metabarcoding data analysis revealed the plant dietary variation of long-tailed macaque Macacafascicularis (Cercopithecidae, Cercopithecinae) living in disturbed habitats in Peninsular Malaysia. Biodivers Data J 2022; 10:e89617. [PMID: 36761533 PMCID: PMC9848512 DOI: 10.3897/bdj.10.e89617] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/09/2022] [Indexed: 11/12/2022] Open
Abstract
The long-tailed macaque (Macacafascicularis) has a wide range in both Peninsular Malaysia and Borneo. Although the primates are especially vulnerable to habitat alterations, this primate lives in disturbed habitats due to human-induced land-use. Thus, this study presents a faecal metabarcoding approach to clarify the plant diet of long-tailed macaques from five locations in Peninsular Malaysia to represent fragmented forest, forest edge, island and recreational park habitats. We extracted genomic DNA from 53 long-tailed macaque faecal samples. We found 47 orders, 126 families, 609 genera and 818 species across these five localities. A total of 113 plant families were consumed by long-tailed macaques in Universiti Kebangsaan Malaysia, 61 in the Malaysia Genome and Vaccine Institute, 33 in Langkawi Island, 53 in Redang Island and 44 in the Cenderawasih Cave. Moraceae (33.24%) and Fabaceae (13.63%) were the most common families consumed by long-tailed macaques from the study localities. We found that habitat type impacted diet composition, indicating the flexibility of foraging activities. This research findings provide an understanding of plant dietary diversity and the adaptability of this macaque with the current alteration level that applies to long-tailed macaque conservation management interest in the future.
Collapse
Affiliation(s)
- Nur Azimah Osman
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia,School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000 Kuala Pilah, Negeri Sembilan, MalaysiaSchool of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan72000 Kuala Pilah, Negeri SembilanMalaysia,Special Interest Group (ECONATREA), School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan, 72000 Kuala Pilah, Negeri Sembilan, MalaysiaSpecial Interest Group (ECONATREA), School of Biology, Faculty of Applied Sciences, Universiti Teknologi Mara Negeri Sembilan72000 Kuala Pilah, Negeri SembilanMalaysia
| | - Muhammad Abu Bakar Abdul-Latiff
- Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus), 84000, Muar, Johor, MalaysiaFaculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia (Pagoh Campus)84000, Muar, JohorMalaysia,Oasis Integrated Group (OIG), Institute for Integrated Engineering (I²E), Universiti Tun Hussein Onn Malaysia, 86400 Parit Raja, Johor, MalaysiaOasis Integrated Group (OIG), Institute for Integrated Engineering (I²E), Universiti Tun Hussein Onn Malaysia86400 Parit Raja, JohorMalaysia
| | - Abd Rahman Mohd-Ridwan
- Centre for Pre-University Studies, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, MalaysiaCentre for Pre-University Studies, Universiti Malaysia Sarawak94300 Kota Samarahan, SarawakMalaysia
| | - Salmah Yaakop
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia
| | - Kayal Vizi Karuppannan
- Department of Wildlife and National Parks (DWNP) KM10, Jalan Cheras, 56100 Kuala Lumpur, MalaysiaDepartment of Wildlife and National Parks (DWNP) KM10, Jalan Cheras56100 Kuala LumpurMalaysia
| | - Badrul Munir Md-Zain
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43000 Bangi, Selangor, MalaysiaDepartment of Biological Sciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia43000 Bangi, SelangorMalaysia
| |
Collapse
|
3
|
Batuecas I, Alomar O, Castañe C, Piñol J, Boyer S, Gallardo-Montoya L, Agustí N. Development of a multiprimer metabarcoding approach to understanding trophic interactions in agroecosystems. INSECT SCIENCE 2022; 29:1195-1210. [PMID: 34905297 DOI: 10.1111/1744-7917.12992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/04/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
To understand trophic interactions and the precise ecological role of each predatory species, it is important to know which arthropod and plant resources are used by generalist predators in agroecosystems. Molecular approaches, such as the use of high-throughput sequencing (HTS), play a key role in identifying these resources. This study develops a multiprimer metabarcoding approach for screening the most common trophic interactions of two predatory arthropods with contrasting morphologies, Rhagonycha fulva (Coleoptera: Cantharidae) and Anthocoris nemoralis (Hemiptera: Anthocoridae) collected from a peach crop. To reduce the time and cost of this metabarcoding approach, we first evaluated the effect of using two different predator-pools of different size (10 and 23 individuals of the same species). We also used our system to analyze the performance of one and two primer pairs in the same library. Our results show that the analysis of 23 individuals together with the use of two primer pairs in the same library optimize the HTS analysis. Using these best-performing conditions, we then analyzed the entire bodies of field-collected predators as well as the washing solutions used to clean the insect bodies. We were able to identify both gut content (i.e., diet) and external pollen load (i.e., on the insects' bodies). This study also demonstrates the importance of washing predatory insects' bodies prior to HTS analysis when the target species have a considerable size (>10 mm) and hairy structures. This metabarcoding approach has significant potential for the study of trophic links in agriculture, revealing expected and unexpected trophic relationships.
Collapse
Affiliation(s)
- Ivan Batuecas
- IRTA, Sustainable Plant Protection, Cabrils, Barcelona, Spain
| | - Oscar Alomar
- IRTA, Sustainable Plant Protection, Cabrils, Barcelona, Spain
| | | | - Josep Piñol
- Universitat Autònoma Barcelona, Cerdanyola del Vallès, Spain
- CREAF, Cerdanyola del Vallès, Spain
| | - Stéphane Boyer
- Institut de Recherche sur la Biologie de l'Insecte (IRBI), Tours University, Tours, France
| | | | - Nuria Agustí
- IRTA, Sustainable Plant Protection, Cabrils, Barcelona, Spain
| |
Collapse
|
4
|
Lee CI, Wang FY, Liu MY, Chou TK, Liao TY. DNA metabarcoding for dietary analysis of Holland's carp (Spinibarbus hollandi) to evaluate the threat to native fishes in Taiwan. JOURNAL OF FISH BIOLOGY 2021; 99:1668-1676. [PMID: 34392529 DOI: 10.1111/jfb.14875] [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] [Received: 12/07/2020] [Revised: 06/20/2021] [Accepted: 08/08/2021] [Indexed: 06/13/2023]
Abstract
DNA metabarcoding analysis for gut contents has been shown to compensate the disadvantage of traditionally morphological identification and offer higher resolution of prey items in an efficient way. Holland's carp (Spinibarbus hollandi) is a freshwater fish native to southern and eastern Taiwan. In the past two decades, this species has been introduced as a sport fish into the river basins of northern and western Taiwan. The large body size and active predation make it a potential threat for native fishes, but which native species are preyed by Holland's carp remains unknown. In this study, the diet from the gut contents of Holland's carp from the Zhonggang River, an invaded basin, was examined using DNA metabarcoding from 51 individuals and by morphological examinations on 140 samples. Detritus of plants were found in 83.6% samples (117 individuals). Twenty fish species of seven families were identified by DNA metabarcoding, including species of all water layers. Taiwan torrent carp (Acrossocheilus paradoxus) and Rhinogobius spp. are the most common prey items. Based on the results of this study, Holland's carp is considered an opportunistic omnivore because of its diverse diet items, which is an important trait for successful invasive fish species. The population decline of Opsariichthys pachycephalus may not result from the invasion of Holland's carps. Nonetheless, the time lag between successful invasion and the samplings of this study may be a concern because the population size of O. pachycephalus may have declined and become difficult to prey. The Holland's carps consumed the least species in winter; nonetheless, the occurrence frequencies of preys among seasons were not significantly different probably because of limited temperature fluctuation. The smallest Holland's carps consumed the least prey species compared to other size categories, similar to the relationship of prey species number to size of invasive largemouth bass (Micropterus salmoides).
Collapse
Affiliation(s)
- Chien-I Lee
- Department of Oceanography, NSYSU, Kaohsiung, Taiwan
| | - Feng-Yu Wang
- Taiwan Ocean Research Institute, Kaohsiung, Taiwan
| | - Min-Yun Liu
- Taiwan Ocean Research Institute, Kaohsiung, Taiwan
| | - Tak-Kei Chou
- Department of Oceanography, NSYSU, Kaohsiung, Taiwan
| | - Te-Yu Liao
- Department of Oceanography, NSYSU, Kaohsiung, Taiwan
| |
Collapse
|
5
|
Building food networks from molecular data: Bayesian or fixed-number thresholds for including links. Basic Appl Ecol 2021. [DOI: 10.1016/j.baae.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
6
|
Němec T, Líznarová E, Birkhofer K, Horsák M. Stable isotope analysis suggests low trophic niche partitioning among co‐occurring land snail species in a floodplain forest. J Zool (1987) 2021. [DOI: 10.1111/jzo.12859] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- T. Němec
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - E. Líznarová
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| | - K. Birkhofer
- Department of Ecology Brandenburg University of Technology Cottbus‐Senftenberg Cottbus Germany
| | - M. Horsák
- Department of Botany and Zoology Faculty of Science Masaryk University Brno Czech Republic
| |
Collapse
|
7
|
Lefort MC, Beggs JR, Glare TR, Saunders TE, Doyle EJ, Boyer S. A molecular approach to study Hymenoptera diets using wasp nests. NEOBIOTA 2020. [DOI: 10.3897/neobiota.63.58640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The study of animal diets has benefited from the rise of high-throughput DNA sequencing applied to stomach content or faecal samples. The latter can be fresh samples used to describe recent meals or older samples, which can provide information about past feeding activities. For most invertebrates, however, it is difficult to access ‘historical’ samples, due to the small size of the animals and the absence of permanent defecation sites. Therefore, sampling must be repeated to account for seasonal variation and to capture the overall diet of a species.
This study develops a method to describe the overall diet of nest-building Hymenoptera, based on a single sampling event, by analysing prey DNA from faeces accumulated in brood cells. We collected 48 nests from two species of introduced paper wasps (Polistes chinensis Fabricius and P. humilis Fabricius) in the urban and peri-urban areas of Auckland, New Zealand and selected two samples per nest. One from brood cells in the outer layer of the nest to represent the most recent diet and one from brood cells in an inner layer to represent older diet.
Diet differed between species, although both fed mainly on Thysanoptera, Lepidoptera and Acariformes. Prey taxa identified to species level included both agricultural pests and native species. Prey communities consumed were significantly different between inner and outer nest samples, suggesting seasonal variation in prey availability and/or a diversification of the wasps’ diet as the colony grows. We also show for the first time potential predation of marine organisms by Polistes wasps.
Our study provides field evidence that Polistes wasps feed on agricultural pests, supporting the hypothesis that some social wasp species could have a suppressing effect on agricultural pests. The proposed methodology is readily applicable to other nest-building Hymenoptera and has the potential to provide comprehensive knowledge about their diet with minimum sampling effort. Such knowledge is essential to measure the ecological impact of invasive Vespidae and support the conservation of native invertebrate biodiversity.
Collapse
|
8
|
Feeding behaviour of red fox and domestic cat populations in suburban areas in the south of Paris. Urban Ecosyst 2020. [DOI: 10.1007/s11252-020-00948-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
9
|
Pustilnik JD. Vertebrate Carrion in Land Snail Diets: First Observation of Amphibian (Plethodontid Salamander) Consumption by a Terrestrial Snail in Southern Appalachia. SOUTHEAST NAT 2020. [DOI: 10.1656/058.019.0106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- Jeremy D. Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, 14850;
| |
Collapse
|
10
|
Nevill PG, Zhong X, Tonti-Filippini J, Byrne M, Hislop M, Thiele K, van Leeuwen S, Boykin LM, Small I. Large scale genome skimming from herbarium material for accurate plant identification and phylogenomics. PLANT METHODS 2020; 16:1. [PMID: 31911810 PMCID: PMC6942304 DOI: 10.1186/s13007-019-0534-5] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Accepted: 11/27/2019] [Indexed: 05/23/2023]
Abstract
BACKGROUND Herbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara. RESULTS Genome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA >> rDNA > matK >> rbcL. CONCLUSIONS We showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.
Collapse
Affiliation(s)
- Paul G. Nevill
- Australian Research Council Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6102 Australia
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Kings Park and Botanic Garden, Fraser Ave, Kings Park, WA 6005 Australia
| | - Xiao Zhong
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Julian Tonti-Filippini
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Margaret Byrne
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
- School of Molecular and Life Sciences, Curtin University, GPO Box U1987, Perth, WA 6102 Australia
| | - Michael Hislop
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Kevin Thiele
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009 Australia
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Stephen van Leeuwen
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Locked Bag 104, Bentley Delivery Centre, Bentley, WA 6983 Australia
| | - Laura M. Boykin
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| | - Ian Small
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, WA 6009 Australia
- School of Molecular Sciences, The University of Western Australia, Crawley, WA 6009 Australia
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
Esnaola A, Arrizabalaga-Escudero A, González-Esteban J, Elosegi A, Aihartza J. Determining diet from faeces: Selection of metabarcoding primers for the insectivore Pyrenean desman (Galemys pyrenaicus). PLoS One 2018; 13:e0208986. [PMID: 30550548 PMCID: PMC6294389 DOI: 10.1371/journal.pone.0208986] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 11/28/2018] [Indexed: 01/06/2023] Open
Abstract
Molecular techniques allow non-invasive dietary studies from faeces, providing an invaluable tool to unveil ecological requirements of endangered or elusive species. They contribute to progress on important issues such as genomics, population genetics, dietary studies or reproductive analyses, essential knowledge for conservation biology. Nevertheless, these techniques require general methods to be tailored to the specific research objectives, as well as to substrate- and species-specific constraints. In this pilot study we test a range of available primers to optimise diet analysis from metabarcoding of faeces of a generalist aquatic insectivore, the endangered Pyrenean desman (Galemys pyrenaicus, É. Geoffroy Saint-Hilaire, 1811, Talpidae), as a step to improve the knowledge of the conservation biology of this species. Twenty-four faeces were collected in the field, DNA was extracted from them, and fragments of the standard barcode region (COI) were PCR amplified by using five primer sets (Brandon-Mong, Gillet, Leray, Meusnier and Zeale). PCR outputs were sequenced on the Illumina MiSeq platform, sequences were processed, clustered into OTUs (Operational Taxonomic Units) using UPARSE algorithm and BLASTed against the NCBI database. Although all primer sets successfully amplified their target fragments, they differed considerably in the amounts of sequence reads, rough OTUs, and taxonomically assigned OTUs. Primer sets consistently identified a few abundant prey taxa, probably representing the staple food of the Pyrenean desman. However, they differed in the less common prey groups. Overall, the combination of Gillet and Zeale primer sets were most cost-effective to identify the widest taxonomic range of prey as well as the desman itself, which could be further improved stepwise by adding sequentially the outputs of Leray, Brandon-Mong and Meusnier primers. These results are relevant for the conservation biology of this endangered species as they allow a better characterization of its food and habitat requirements.
Collapse
Affiliation(s)
- Amaiur Esnaola
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
- * E-mail:
| | - Aitor Arrizabalaga-Escudero
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
| | | | - Arturo Elosegi
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, Basque Country, Spain
| |
Collapse
|
13
|
Bell BD, Easton LJ, Walker KJ, Woolley CK. Physical contact between a native frog (Leiopelma pakeka) and a carnivorous land snail (Powelliphanta hochstetteri obscura): what was going on? NEW ZEALAND JOURNAL OF ZOOLOGY 2018. [DOI: 10.1080/03014223.2018.1538055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Ben D. Bell
- Centre for Biodiversity & Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| | - Luke J. Easton
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Kath J. Walker
- Nelson Office, Department of Conservation, Nelson, New Zealand
| | - Christopher K. Woolley
- Centre for Biodiversity & Restoration Ecology, School of Biological Sciences, Victoria University of Wellington, Wellington, New Zealand
| |
Collapse
|
14
|
Fernandes K, van der Heyde M, Bunce M, Dixon K, Harris RJ, Wardell-Johnson G, Nevill PG. DNA metabarcoding-a new approach to fauna monitoring in mine site restoration. Restor Ecol 2018. [DOI: 10.1111/rec.12868] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristen Fernandes
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Kingsley Dixon
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Richard J. Harris
- School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Grant Wardell-Johnson
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| | - Paul G. Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences; Curtin University; GPO Box U1987, Perth WA 6102 Australia
| |
Collapse
|
15
|
A comparison of next-generation sequencing with clone sequencing in the diet analysis of Asian great bustard. CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0952-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
16
|
Nielsen JM, Clare EL, Hayden B, Brett MT, Kratina P. Diet tracing in ecology: Method comparison and selection. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12869] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Jens M. Nielsen
- School of Biological and Chemical SciencesQueen Mary University of London London UK
| | - Elizabeth L. Clare
- School of Biological and Chemical SciencesQueen Mary University of London London UK
| | - Brian Hayden
- Canadian Rivers InstituteBiology DepartmentUniversity of New Brunswick Fredericton NB Canada
| | - Michael T. Brett
- Department of Civil and Environmental EngineeringUniversity of Washington Seattle WA USA
| | - Pavel Kratina
- School of Biological and Chemical SciencesQueen Mary University of London London UK
| |
Collapse
|
17
|
Olmos-Pérez L, Roura Á, Pierce GJ, Boyer S, González ÁF. Diet Composition and Variability of Wild Octopus vulgaris and Alloteuthis media (Cephalopoda) Paralarvae: a Metagenomic Approach. Front Physiol 2017; 8:321. [PMID: 28596735 PMCID: PMC5442249 DOI: 10.3389/fphys.2017.00321] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
The high mortality of cephalopod early stages is the main bottleneck to grow them from paralarvae to adults in culture conditions, probably because the inadequacy of the diet that results in malnutrition. Since visual analysis of digestive tract contents of paralarvae provides little evidence of diet composition, the use of molecular tools, particularly next generation sequencing (NGS) platforms, offers an alternative to understand prey preferences and nutrient requirements of wild paralarvae. In this work, we aimed to determine the diet of paralarvae of the loliginid squid Alloteuthis media and to enhance the knowledge of the diet of recently hatched Octopus vulgaris paralarvae collected in different areas and seasons in an upwelling area (NW Spain). DNA from the dissected digestive glands of 32 A. media and 64 O. vulgaris paralarvae was amplified with universal primers for the mitochondrial gene COI, and specific primers targeting the mitochondrial gene 16S gene of arthropods and the mitochondrial gene 16S of Chordata. Following high-throughput DNA sequencing with the MiSeq run (Illumina), up to 4,124,464 reads were obtained and 234,090 reads of prey were successfully identified in 96.87 and 81.25% of octopus and squid paralarvae, respectively. Overall, we identified 122 Molecular Taxonomic Units (MOTUs) belonging to several taxa of decapods, copepods, euphausiids, amphipods, echinoderms, molluscs, and hydroids. Redundancy analysis (RDA) showed seasonal and spatial variability in the diet of O. vulgaris and spatial variability in A. media diet. General Additive Models (GAM) of the most frequently detected prey families of O. vulgaris revealed seasonal variability of the presence of copepods (family Paracalanidae) and ophiuroids (family Euryalidae), spatial variability in presence of crabs (family Pilumnidae) and preference in small individual octopus paralarvae for cladocerans (family Sididae) and ophiuroids. No statistically significant variation in the occurrences of the most frequently identified families was revealed in A. media. Overall, these results provide new clues about dietary preferences of wild cephalopod paralarvae, thus opening up new scenarios for research on trophic ecology and digestive physiology under controlled conditions.
Collapse
Affiliation(s)
| | - Álvaro Roura
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain.,La Trobe UniversityMelbourne, VIC, Australia
| | - Graham J Pierce
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain.,CESAM and Departamento de Biologia, Universidade de AveiroAveiro, Portugal
| | - Stéphane Boyer
- Applied Molecular Solutions Research Group, Environmental and Animal Sciences, Unitec Institute of TechnologyAuckland, New Zealand
| | - Ángel F González
- Instituto de Investigaciones Marinas, Ecobiomar, CSICVigo, Spain
| |
Collapse
|
18
|
Hoso M. Asymmetry of mandibular dentition is associated with dietary specialization in snail-eating snakes. PeerJ 2017; 5:e3011. [PMID: 28265502 PMCID: PMC5337109 DOI: 10.7717/peerj.3011] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/21/2017] [Indexed: 01/08/2023] Open
Abstract
Background In vertebrates, the left-and-right pairs of homologous organs are generally present in equal numbers. A remarkable exception is snail-eating snakes in the family Pareidae: almost all the pareid snakes have much more teeth on the right mandible than on the left for functional specialization in feeding on the dextral majority of land snails. Because the only exceptional species with symmetric dentition has been regarded as a slug-eater, the extent of dietary specialization on slugs could shape the degree of the lateral asymmetry of mandibular dentition (dentition asymmetry) even among snail eaters. Methods To test this, I compared the morphology and behavior of two sympatric species of Taiwanese snail-eating snakes, Pareas atayal and P. formosensis. Results Specimens collected in the same locality showed that the dentition asymmetry of P. formosensis was significantly smaller than that of P. atayal. Congruent to its weak asymmetry, P. formosensis showed a strong preference of slugs to snails in the feeding experiment. Discussion The dietary specialization of P. formosensis on slugs would contribute to niche partitioning from the sympatric congener P. atayal. This study suggests that the diverse variation in the dentition asymmetry of pareid snakes is the result of their dietary specialization and divergence.
Collapse
Affiliation(s)
- Masaki Hoso
- Hakubi Center for Advanced Research, Kyoto University, Kyoto, Japan; Department of Zoology/Graduate School of Science, Kyoto University, Kyoto, Japan
| |
Collapse
|
19
|
Khanam S, Howitt R, Mushtaq M, Russell JC. Diet analysis of small mammal pests: A comparison of molecular and microhistological methods. Integr Zool 2016; 11:98-110. [PMID: 27001489 DOI: 10.1111/1749-4877.12172] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Knowledge of what pest species are eating is important to determine their impact on stored food products and to plan management strategies accordingly. In this study, we investigated the food habits of 2 rodents, Rattus rattus (ship rat) and Mus musculus castaneus (house mouse) as well as an insectivore, Suncus murinus (shrew), present in human dwellings. Both a microhistological approach and a DNA barcoding approach were used in the present study. Following DNA extraction, amplification was performed using group-specific primers targeting birds, plants and invertebrates. Resulting polymerase chain reaction products were sequenced and analyzed to identify the different prey species present in the gut contents. The findings from the application of both techniques were in agreement, but the detection of prey type with each technique was different. The DNA barcoding approach gave greater species-level identification when compared to the microhistological method, especially for the invertebrate and avian prey. Overall, with both techniques, 23 prey taxa were identified in the gut contents of the 3 species, including 15 plants, 7 insects and a single bird species. We conclude that with a selection of suitable "barcode genes" and optimization of polymerase chain reaction protocols, DNA barcoding can provide more accurate and faster results. Prey detection from either technique alone can bias the dietary information. Hence, combining prey information of both microhistological analysis and DNA barcoding is recommended to study pest diet, especially if the pest is an omnivore or insectivore species.
Collapse
Affiliation(s)
- Surrya Khanam
- Department of Zoology, PMAS Arid Agriculture University Rawalpindi, Pakistan
| | - Robyn Howitt
- EcoGene®, Landcare Research, Auckland, New Zealand
| | - Muhammad Mushtaq
- Department of Zoology, PMAS Arid Agriculture University Rawalpindi, Pakistan
| | - James C Russell
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.,Department of Statistics, University of Auckland, Auckland, New Zealand.,Allan Wilson Centre, University of Auckland, Auckland, New Zealand
| |
Collapse
|
20
|
Iwanowicz DD, Vandergast AG, Cornman RS, Adams CR, Kohn JR, Fisher RN, Brehme CS. Metabarcoding of Fecal Samples to Determine Herbivore Diets: A Case Study of the Endangered Pacific Pocket Mouse. PLoS One 2016; 11:e0165366. [PMID: 27851756 PMCID: PMC5112926 DOI: 10.1371/journal.pone.0165366] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 10/11/2016] [Indexed: 11/24/2022] Open
Abstract
Understanding the diet of an endangered species illuminates the animal’s ecology, habitat requirements, and conservation needs. However, direct observation of diet can be difficult, particularly for small, nocturnal animals such as the Pacific pocket mouse (Heteromyidae: Perognathus longimembris pacificus). Very little is known of the dietary habits of this federally endangered rodent, hindering management and restoration efforts. We used a metabarcoding approach to identify source plants in fecal samples (N = 52) from the three remaining populations known. The internal transcribed spacers (ITS) of the nuclear ribosomal loci were sequenced following the Illumina MiSeq amplicon strategy and processed reads were mapped to reference databases. We evaluated a range of threshold mapping criteria and found the best-performing setting generally recovered two distinct mock communities in proportions similar to expectation. We tested our method on captive animals fed a known diet and recovered almost all plant sources, but found substantial heterogeneity among fecal pellets collected from the same individual at the same time. Observed richness did not increase with pooling of pellets from the same individual. In field-collected samples, we identified 4–14 plant genera in individual samples and 74 genera overall, but over 50 percent of reads mapped to just six species in five genera. We simulated the effects of sequencing error, variable read length, and chimera formation to infer taxon-specific rates of misassignment for the local flora, which were generally low with some exceptions. Richness at the species and genus levels did not reach a clear asymptote, suggesting that diet breadth remained underestimated in the current pool of samples. Large numbers of scat samples are therefore needed to make inferences about diet and resource selection in future studies of the Pacific pocket mouse. We conclude that our minimally invasive method is promising for determining herbivore diets given a library of sequences from local plants.
Collapse
Affiliation(s)
- Deborah D. Iwanowicz
- U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, United States of America
- * E-mail:
| | - Amy G. Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Robert S. Cornman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, United States of America
| | - Cynthia R. Adams
- U.S. Geological Survey, Leetown Science Center, Kearneysville, West Virginia, United States of America
| | - Joshua R. Kohn
- University of California San Diego, Division of Biological Sciences, La Jolla, California, United States of America
| | - Robert N. Fisher
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| | - Cheryl S. Brehme
- U.S. Geological Survey, Western Ecological Research Center, San Diego, California, United States of America
| |
Collapse
|
21
|
Boyer S, Kim YN, Bowie MH, Lefort MC, Dickinson NM. Response of endemic and exotic earthworm communities to ecological restoration. Restor Ecol 2016. [DOI: 10.1111/rec.12416] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stéphane Boyer
- Environmental and Animal Sciences; Unitec Institute of Technology; Private Bag 92025, Victoria Street West Auckland 1142 New Zealand
- Bio-Protection Research Centre; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
- Department of Ecology, Faculty of Agriculture and Life Sciences; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
| | - Young-Nam Kim
- Department of Ecology, Faculty of Agriculture and Life Sciences; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
| | - Mike H. Bowie
- Department of Ecology, Faculty of Agriculture and Life Sciences; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
| | - Marie-Caroline Lefort
- Environmental and Animal Sciences; Unitec Institute of Technology; Private Bag 92025, Victoria Street West Auckland 1142 New Zealand
- Bio-Protection Research Centre; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
| | - Nicholas M. Dickinson
- Department of Ecology, Faculty of Agriculture and Life Sciences; Lincoln University; PO Box 85084 Lincoln 7647 New Zealand
| |
Collapse
|
22
|
Sousa LL, Xavier R, Costa V, Humphries NE, Trueman C, Rosa R, Sims DW, Queiroz N. DNA barcoding identifies a cosmopolitan diet in the ocean sunfish. Sci Rep 2016; 6:28762. [PMID: 27373803 PMCID: PMC4931451 DOI: 10.1038/srep28762] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/07/2016] [Indexed: 01/30/2023] Open
Abstract
The ocean sunfish (Mola mola) is the world’s heaviest bony fish reaching a body mass of up to 2.3 tonnes. However, the prey M. mola consumes to fuel this prodigious growth remains poorly known. Sunfish were thought to be obligate gelatinous plankton feeders, but recent studies suggest a more generalist diet. In this study, through molecular barcoding and for the first time, the diet of sunfish in the north-east Atlantic Ocean was characterised. Overall, DNA from the diet content of 57 individuals was successfully amplified, identifying 41 different prey items. Sunfish fed mainly on crustaceans and teleosts, with cnidarians comprising only 16% of the consumed prey. Although no adult fishes were sampled, we found evidence for an ontogenetic shift in the diet, with smaller individuals feeding mainly on small crustaceans and teleost fish, whereas the diet of larger fish included more cnidarian species. Our results confirm that smaller sunfish feed predominantly on benthic and on coastal pelagic species, whereas larger fish depend on pelagic prey. Therefore, sunfish is a generalist predator with a greater diversity of links in coastal food webs than previously realised. Its removal as fisheries’ bycatch may have wider reaching ecological consequences, potentially disrupting coastal trophic interactions.
Collapse
Affiliation(s)
- Lara L Sousa
- CIBIO - Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-668 Vairão, Portugal.,Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Raquel Xavier
- CIBIO - Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-668 Vairão, Portugal.,School of Biological Sciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - Vânia Costa
- CIBIO - Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-668 Vairão, Portugal.,Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Nicolas E Humphries
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Clive Trueman
- Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK
| | - Rui Rosa
- MARE - Marine and Environmental Sciences Centre, Laboratório Marítimo da Guia, Faculdade de Ciências da Universidade de Lisboa, Av. Nossa Senhora do Cabo, 939, 2750-374 Cascais, Portugal
| | - David W Sims
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK.,Ocean and Earth Science, University of Southampton, Waterfront Campus, European Way, Southampton SO14 3ZH, UK.,Centre for Biological Sciences, Building 85, University of Southampton, Highfield Campus, Southampton SO17 1BJ, UK
| | - Nuno Queiroz
- CIBIO - Universidade do Porto, Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-668 Vairão, Portugal
| |
Collapse
|
23
|
Roslin T, Majaneva S. The use of DNA barcodes in food web construction-terrestrial and aquatic ecologists unite! Genome 2016; 59:603-28. [PMID: 27484156 DOI: 10.1139/gen-2015-0229] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
By depicting who eats whom, food webs offer descriptions of how groupings in nature (typically species or populations) are linked to each other. For asking questions on how food webs are built and work, we need descriptions of food webs at different levels of resolution. DNA techniques provide opportunities for highly resolved webs. In this paper, we offer an exposé of how DNA-based techniques, and DNA barcodes in particular, have recently been used to construct food web structure in both terrestrial and aquatic systems. We highlight how such techniques can be applied to simultaneously improve the taxonomic resolution of the nodes of the web (i.e., the species), and the links between them (i.e., who eats whom). We end by proposing how DNA barcodes and DNA information may allow new approaches to the construction of larger interaction webs, and overcome some hurdles to achieving adequate sample size. Most importantly, we propose that the joint adoption and development of these techniques may serve to unite approaches to food web studies in aquatic and terrestrial systems-revealing the extent to which food webs in these environments are structured similarly to or differently from each other, and how they are linked by dispersal.
Collapse
Affiliation(s)
- Tomas Roslin
- a Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, 750 07 Uppsala, Sweden.,b Spatial Foodweb Ecology Group, Department of Agricultural Sciences, PO Box 27, (Latokartanonkaari 5), FI-00014 University of Helsinki, Finland
| | - Sanna Majaneva
- c Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Department of Biology and Environmental Science, Linnaeus University, 39182 Kalmar, Sweden
| |
Collapse
|
24
|
Omnivory of an Insular Lizard: Sources of Variation in the Diet of Podarcis lilfordi (Squamata, Lacertidae). PLoS One 2016; 11:e0148947. [PMID: 26871439 PMCID: PMC4752353 DOI: 10.1371/journal.pone.0148947] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022] Open
Abstract
Through 17 years and from a sample of 7,790 faecal pellets and 26,346 prey items, we studied the diet of the Balearic lizard Podarcis lilfordi in Aire Island (Menorca, Balearic Islands, Spain). We analysed the diet in terms of prey frequencies, as well as by their volume and biomass contributions. The diet of the Balearic lizard was extremely variable through the years, months and areas under study. The dominance of small clumped prey, particularly ants, was confirmed. However, the main contribution by volume corresponded to beetles, with a relevant role for Diplopoda and terrestrial Isopoda during some months and at particular areas of the island. Several prey items were probably captured at the base of shrubs, under stones or inside rock crevices. Therefore, our estimations of electivity would only be reliable for epigeal and flying prey. The capacity of the Balearic lizard to include marine subsidies in its diet, such as coastal crustaceans, is noteworthy. Also, its consumption of carrion from carcasses of gulls and rabbits and leftovers from human visitors is remarkable. Juvenile conspecifics can also be a sporadic food resource, especially during the second half of summer, whereas the consumption of vegetal matter is constant for each whole year. The shifts of vegetal exploitation among areas of the island and months take place according to availability of different plant species at each area or during a given period. Thus, lizards are able to conduct a thorough monitoring of plant phenology, exploiting a large variety of plant species. Omnivory does not imply the indiscriminate inclusion of any edible food in its diet. Rather, the inclusion of several food items means the adoption of a wide range of foraging behaviours adapted to the exploitation of each food resource.
Collapse
|
25
|
Vacher C, Tamaddoni-Nezhad A, Kamenova S, Peyrard N, Moalic Y, Sabbadin R, Schwaller L, Chiquet J, Smith MA, Vallance J, Fievet V, Jakuschkin B, Bohan DA. Learning Ecological Networks from Next-Generation Sequencing Data. ADV ECOL RES 2016. [DOI: 10.1016/bs.aecr.2015.10.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
26
|
McClenaghan B, Gibson JF, Shokralla S, Hajibabaei M. Discrimination of grasshopper (Orthoptera: Acrididae) diet and niche overlap using next-generation sequencing of gut contents. Ecol Evol 2015; 5:3046-55. [PMID: 26356479 PMCID: PMC4559048 DOI: 10.1002/ece3.1585] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 06/04/2015] [Accepted: 06/05/2015] [Indexed: 11/10/2022] Open
Abstract
Species of grasshopper have been divided into three diet classifications based on mandible morphology: forbivorous (specialist on forbs), graminivorous (specialist on grasses), and mixed feeding (broad-scale generalists). For example, Melanoplus bivittatus and Dissosteira carolina are presumed to be broad-scale generalists, Chortophaga viridifasciata is a specialist on grasses, and Melanoplus femurrubrum is a specialist on forbs. These classifications, however, have not been verified in the wild. Multiple specimens of these four species were collected, and diet analysis was performed using DNA metabarcoding of the gut contents. The rbcLa gene region was amplified and sequenced using Illumina MiSeq sequencing. Levins' measure and the Shannon-Wiener measure of niche breadth were calculated using family-level identifications and Morisita's measure of niche overlap was calculated using operational taxonomic units (OTUs). Gut contents confirm both D. carolina and M. bivittatus as generalists and C. viridifasciata as a specialist on grasses. For M. femurrubrum, a high niche breadth was observed and species of grasses were identified in the gut as well as forbs. Niche overlap values did not follow predicted patterns, however, the low values suggest low competition between these species.
Collapse
Affiliation(s)
- Beverly McClenaghan
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of GuelphGuelph, N1G 2W1, Ontario, Canada
| | - Joel F Gibson
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of GuelphGuelph, N1G 2W1, Ontario, Canada
| | - Shadi Shokralla
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of GuelphGuelph, N1G 2W1, Ontario, Canada
| | - Mehrdad Hajibabaei
- Department of Integrative Biology, Biodiversity Institute of Ontario, University of GuelphGuelph, N1G 2W1, Ontario, Canada
| |
Collapse
|
27
|
Boyer S, Cruickshank RH, Wratten SD. Faeces of generalist predators as ‘biodiversity capsules’: A new tool for biodiversity assessment in remote and inaccessible habitats. FOOD WEBS 2015. [DOI: 10.1016/j.fooweb.2015.02.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
28
|
Clare EL. Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications. Evol Appl 2014; 7:1144-57. [PMID: 25553074 PMCID: PMC4231602 DOI: 10.1111/eva.12225] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 08/21/2014] [Indexed: 02/06/2023] Open
Abstract
The emerging field of ecological genomics contains several broad research areas. Comparative genomic and conservation genetic analyses are providing great insight into adaptive processes, species bottlenecks, population dynamics and areas of conservation priority. Now the same technological advances in high-throughput sequencing, coupled with taxonomically broad sequence repositories, are providing greater resolution and fundamentally new insights into functional ecology. In particular, we now have the capacity in some systems to rapidly identify thousands of species-level interactions using non-invasive methods based on the detection of trace DNA. This represents a powerful tool for conservation biology, for example allowing the identification of species with particularly inflexible niches and the investigation of food-webs or interaction networks with unusual or vulnerable dynamics. As they develop, these analyses will no doubt provide significant advances in the field of restoration ecology and the identification of appropriate locations for species reintroduction, as well as highlighting species at ecological risk. Here, I describe emerging patterns that have come from the various initial model systems, the advantages and limitations of the technique and key areas where these methods may significantly advance our empirical and applied conservation practices.
Collapse
Affiliation(s)
- Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London London, UK
| |
Collapse
|
29
|
Egeter B, Bishop PJ, Robertson BC. Detecting frogs as prey in the diets of introduced mammals: a comparison between morphological and DNA-based diet analyses. Mol Ecol Resour 2014; 15:306-16. [DOI: 10.1111/1755-0998.12309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 01/25/2023]
Affiliation(s)
- Bastian Egeter
- Department of Zoology; University of Otago; PO Box 56 Dunedin New Zealand
| | - Phillip J. Bishop
- Department of Zoology; University of Otago; PO Box 56 Dunedin New Zealand
| | - Bruce C. Robertson
- Department of Zoology; University of Otago; PO Box 56 Dunedin New Zealand
- Allan Wilson Centre for Molecular Ecology and Evolution; Department of Zoology; University of Otago; PO Box 56, Dunedin New Zealand
| |
Collapse
|
30
|
Waterhouse BR, Boyer S, Wratten SD. Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes. Oecologia 2014; 175:737-46. [PMID: 24668016 DOI: 10.1007/s00442-014-2933-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/12/2014] [Indexed: 10/25/2022]
Abstract
Identifying and understanding predator diets is of high importance in biological conservation. This is particularly true for the introduction, establishment and maintenance of predator populations in newly created or modified ecological communities, such as translocation sites or restored habitats. Conservation status of predators may not permit captive feeding trials or intrusive gut-content methods, so non-intrusive diet assessment is required, such as faecal analysis. However, prey such as earthworms leave no morphological clues suitable for accurately discriminating between species consumed through visual faecal analysis. This study uses non-intrusive molecular methods on earthworm DNA extracted from the faeces of the carnivorous land snail Powelliphanta patrickensis to identify its earthworm diet and any seasonal trends. Data from 454-pyrosequencing revealed earthworm DNA in all samples (n = 60). Sequences were compared to a DNA library created from published and unpublished studies of New Zealand's endemic earthworms and online databases. Unidentified earthworm sequences were clustered into molecular operational taxonomic units (MOTUs). Twenty-six MOTUs were identified, 17 of which matched the library, whereas nine did not. Similarity indices indicate that there were seasonal differences (P < 0.05) in the earthworm communities represented in the summer and the winter diets. This study highlights the importance of utilising the vast body of data generated by pyrosequencing to investigate potential temporal diet shifts in protected species. The method described here is widely applicable to a wide range of predatory species of conservation interest and can further inform habitat restoration and relocation programmes to optimize the long-term survival of the target species.
Collapse
Affiliation(s)
- Benjamin R Waterhouse
- Bio-Protection Research Centre, Lincoln University, P.O. Box 85084, Lincoln, 7647, New Zealand,
| | | | | |
Collapse
|