1
|
Stenhouse EH, Bellamy P, Kirby W, Vaughan IP, Drake LE, Marchbank A, Workman T, Symondson WOC, Orozco‐terWengel P. Multi-marker DNA metabarcoding reveals spatial and sexual variation in the diet of a scarce woodland bird. Ecol Evol 2023; 13:e10089. [PMID: 37206688 PMCID: PMC10191781 DOI: 10.1002/ece3.10089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 04/24/2023] [Accepted: 04/28/2023] [Indexed: 05/21/2023] Open
Abstract
Avian diet can be affected by site-specific variables, such as habitat, as well as intrinsic factors such as sex. This can lead to dietary niche separation, which reduces competition between individuals, as well as impacting how well avian species can adapt to environmental variation. Estimating dietary niche separation is challenging, due largely to difficulties in accurately identifying food taxa consumed. Consequently, there is limited knowledge of the diets of woodland bird species, many of which are undergoing serious population declines. Here, we show the effectiveness of multi-marker fecal metabarcoding to provide in-depth dietary analysis of a declining passerine in the UK, the Hawfinch (Coccothraustes coccothraustes). We collected fecal samples from (n = 262) UK Hawfinches prior to, and during, the breeding seasons in 2016-2019. We detected 49 and 90 plant and invertebrate taxa, respectively. We found Hawfinch diet varied spatially, as well as between sexes, indicating broad dietary plasticity and the ability of Hawfinches to utilize multiple resources within their foraging environments.
Collapse
Affiliation(s)
- Ewan H. Stenhouse
- School of BiosciencesCardiff UniversityCardiffUK
- RSPB Centre for Conservation Science, The LodgeSandyUK
| | - Paul Bellamy
- RSPB Centre for Conservation Science, The LodgeSandyUK
| | - Will Kirby
- RSPB Centre for Conservation Science, The LodgeSandyUK
| | | | | | | | | | | | | |
Collapse
|
2
|
Browett SS, Synnott R, O'Meara DB, Antwis RE, Browett SS, Bown KJ, Wangensteen OS, Dawson DA, Searle JB, Yearsley JM, McDevitt AD. Resource competition drives an invasion-replacement event among shrew species on an island. J Anim Ecol 2023; 92:698-709. [PMID: 36617677 DOI: 10.1111/1365-2656.13855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 11/17/2022] [Indexed: 01/10/2023]
Abstract
Invasive mammals are responsible for the majority of native species extinctions on islands. While most of these extinction events will be due to novel interactions between species (e.g. exotic predators and naive prey), it is more unusual to find incidences where a newly invasive species causes the decline/extinction of a native species on an island when they normally coexist elsewhere in their overlapping mainland ranges. We investigated if resource competition between two insectivorous small mammals was playing a significant role in the rapid replacement of the native pygmy shrew Sorex minutus in the presence of the recently invading greater white-toothed shrew Crocidura russula on the island of Ireland. We used DNA metabarcoding of gut contents from >300 individuals of both species to determine each species' diet and measured the body size (weight and length) during different stages of the invasion in Ireland (before, during and after the species come into contact with one another) and on a French island where both species have long coexisted (acting as a natural 'control' site). Dietary composition, niche width and overlap and body size were compared in these different stages. The body size of the invasive C. russula and composition of its diet changes between when it first invades an area and after it becomes established. During the initial stages of the invasion, individual shrews are larger and consume larger sized invertebrate prey species. During later stages of the invasion, C. russula switches to consuming smaller prey taxa that are more essential for the native species. As a result, the level of interspecific dietary overlap increases from between 11% and 14% when they first come into contact with each other to between 39% and 46% after the invasion. Here we show that an invasive species can quickly alter its dietary niche in a new environment, ultimately causing the replacement of a native species. In addition, the invasive shrew could also be potentially exhausting local resources of larger invertebrate species. These subsequent changes in terrestrial invertebrate communities could have severe impacts further downstream on ecosystem functioning and services.
Collapse
Affiliation(s)
- Samuel S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland.,NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Rebecca Synnott
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Denise B O'Meara
- Molecular Ecology Research Group, Eco-Innovation Research Centre, School of Science and Computing, South East Technological University, Waterford, Ireland
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Stephen S Browett
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Kevin J Bown
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Owen S Wangensteen
- Norwegian College of Fishery Science, University of Tromsø, Tromsø, Norway
| | - Deborah A Dawson
- NERC Environmental Omics Facility, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Jeremy B Searle
- Department of Ecology and Evolution, Corson Hall, Cornell University, Ithaca, New York, USA
| | - Jon M Yearsley
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - Allan D McDevitt
- School of Science, Engineering and Environment, University of Salford, Salford, UK.,Department of Natural Sciences and the Environment, School of Science and Computing, Atlantic Technological University, Galway, Ireland
| |
Collapse
|
3
|
Gong L, Gu H, Chang Y, Wang Z, Shi B, Lin A, Wu H, Feng J, Jiang T. Seasonal variation of population and individual dietary niche in the avivorous bat, Ia io. Oecologia 2023; 201:733-747. [PMID: 36929223 DOI: 10.1007/s00442-023-05346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
The variation in niche breadth can affect how species respond to environmental and resource changes. However, there is still no clear understanding of how seasonal variability in food resources impacts the variation of individual dietary diversity, thereby affecting the dynamics of a population's dietary niche breadth. Optimal foraging theory (OFT) and the niche variation hypothesis (NVH) predict that when food resources are limited, the population niche breadth will widen or narrow due to increased within-individual dietary diversity and individual specialization or reduced within-individual dietary diversity, respectively. Here, we used DNA metabarcoding to examine the composition and seasonality of diets of the avivorous bat Ia io. Furthermore, we investigated how the dietary niches changed among seasons and how the population niche breadth changed when the availability of insect resources was reduced in autumn. We found that there was differentiation in dietary niches among seasons and a low degree of overlap, and the decrease of insect resource availability and the emergence of ecological opportunities of nocturnal migratory birds might drive dietary niche shifts toward birds in I. io. However, the population's dietary niche breadth did not broaden by increasing the within-individual dietary diversity or individual specialization, but rather became narrower by reducing dietary diversity via predation on bird resources that served as an ecological opportunity when insect resources were scarce in autumn. Our findings were consistent with the predictions of OFT, because birds as prey for bats provided extremely different resources from those of insects in size and nutritional value. Our work highlights the importance of size and quality of prey resources along with other factors (i.e., physiological, behavioral, and life-history traits) in dietary niche variation.
Collapse
Affiliation(s)
- Lixin Gong
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Hao Gu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Yang Chang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Zhiqiang Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Biye Shi
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Hui Wu
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.
- College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.
- Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.
| |
Collapse
|
4
|
Effect of diet on gut microbiota diversity in mandarin ducks (Aix galericulata) revealed by Illumina high-throughput sequencing. Arch Microbiol 2022; 204:725. [DOI: 10.1007/s00203-022-03333-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 11/27/2022]
|
5
|
Villsen K, Corse E, Meglécz E, Archambaud‐Suard G, Vignes H, Ereskovsky AV, Chappaz R, Dubut V. DNA metabarcoding suggests adaptive seasonal variation of individual trophic traits in a critically endangered fish. Mol Ecol 2022; 31:5889-5908. [PMID: 36125278 PMCID: PMC9828795 DOI: 10.1111/mec.16698] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 09/12/2022] [Accepted: 09/15/2022] [Indexed: 01/13/2023]
Abstract
Dietary studies are critical for understanding foraging strategies and have important applications in conservation and habitat management. We applied a robust metabarcoding protocol to characterize the diet of the critically endangered freshwater fish Zingel asper (the Rhone streber). We conducted modelling and simulation analyses to identify and characterize some of the drivers of individual trophic trait variation in this species. We found that population density and ontogeny had minor effects on the trophic niche of Z. asper. Instead, our results suggest that the majority of trophic niche variation was driven by seasonal variation in ecological opportunity. The total trophic niche width of Z. asper seasonally expanded to include a broader range of prey. Furthermore, null model simulations revealed that the increase of between-individual variation in autumn indicates that Z. asper become more opportunistic relative to summer and spring, rather than being associated with a seasonal specialization of individuals. Overall, our results suggest an adaptive variation of individual trophic traits in Z. asper: the species mainly consumes a few ephemeropteran taxa (Baetis fuscatus and Ecdyonurus) but seems to be capable of adapting its foraging strategy to maintain its body condition. This study illustrates how metabarcoding data obtained from faeces can be validated and combined with individual-based modelling and simulation approaches to explore inter- and intrapopulational individual trophic traits variation and to test hypotheses in the conventional analytic framework of trophic ecology.
Collapse
Affiliation(s)
- Kurt Villsen
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | - Emmanuel Corse
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,Centre Universitaire de Formation et de Recherche de Mayotte (CUFR)DembeniFrance,MARBEC, University of Montpellier, CNRS, Ifremer, IRDMontpellierFrance
| | - Emese Meglécz
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| | | | - Hélène Vignes
- CIRAD, University of Montpellier, INRAE, Montpellier SupAgro, AGAPMontpellierFrance
| | - Alexander V. Ereskovsky
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance,St. Petersburg State UniversitySt. PetersburgRussia,Koltzov Institute of Developmental Biology of Russian Academy of SciencesMoscowRussia
| | - Rémi Chappaz
- INRAE, Aix Marseille Université, RECOVERAix‐en‐ProvenceFrance
| | - Vincent Dubut
- Aix Marseille Université, CNRS, IRDAvignon Université, IMBEMarseilleFrance
| |
Collapse
|
6
|
Davies SR, Vaughan IP, Thomas RJ, Drake LE, Marchbank A, Symondson WOC. Seasonal and ontological variation in diet and age-related differences in prey choice, by an insectivorous songbird. Ecol Evol 2022; 12:e9180. [PMID: 35979519 PMCID: PMC9366593 DOI: 10.1002/ece3.9180] [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: 06/24/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/09/2022] Open
Abstract
The diet of an individual animal is subject to change over time, both in response to short-term food fluctuations and over longer time scales as an individual ages and meets different challenges over its life cycle. A metabarcoding approach was used to elucidate the diet of different life stages of a migratory songbird, the Eurasian reed warbler (Acrocephalus scirpaceus) over the 2017 summer breeding season in Somerset, the United Kingdom. The feces of adult, juvenile, and nestling warblers were screened for invertebrate DNA, enabling the identification of prey species. Dietary analysis was coupled with monitoring of Diptera in the field using yellow sticky traps. Seasonal changes in warbler diet were subtle, whereas age class had a greater influence on overall diet composition. Age classes showed high dietary overlap, but significant dietary differences were mediated through the selection of prey; (i) from different taxonomic groups, (ii) with different habitat origins (aquatic vs. terrestrial), and (iii) of different average approximate sizes. Our results highlight the value of metabarcoding data for enhancing ecological studies of insectivores in dynamic environments.
Collapse
Affiliation(s)
- Sarah R Davies
- Cardiff School of Biosciences Cardiff University Cardiff UK
| | - Ian P Vaughan
- Cardiff School of Biosciences Cardiff University Cardiff UK
| | | | - Lorna E Drake
- Cardiff School of Biosciences Cardiff University Cardiff UK
| | | | | |
Collapse
|
7
|
Nordstrom B, Mitchell N, Byrne M, Jarman S. A review of applications of environmental DNA for reptile conservation and management. Ecol Evol 2022; 12:e8995. [PMID: 35784065 PMCID: PMC9168342 DOI: 10.1002/ece3.8995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/28/2022] Open
Abstract
Reptile populations are in decline globally, with total reptile abundance halving in the past half century, and approximately a fifth of species currently threatened with extinction. Research on reptile distributions, population trends, and trophic interactions can greatly improve the accuracy of conservation listings and planning for species recovery, but data deficiency is an impediment for many species. Environmental DNA (eDNA) can detect species and measure community diversity at diverse spatio‐temporal scales, and is especially useful for detection of elusive, cryptic, or rare species, making it potentially very valuable in herpetology. We aim to summarize the utility of eDNA as a tool for informing reptile conservation and management and discuss the benefits and limitations of this approach. A literature review was conducted to collect all studies that used eDNA and focus on reptile ecology, conservation, or management. Results of the literature search are summarized into key discussion points, and the review also draws on eDNA studies from other taxa to highlight methodological challenges and to identify future research directions. eDNA has had limited application to reptiles, relative to other vertebrate groups, and little use in regions with high species richness. eDNA techniques have been more successfully applied to aquatic reptiles than to terrestrial reptiles, and most (64%) of studies focused on aquatic habitats. Two of the four reptilian orders dominate the existing eDNA studies (56% Testudines, 49% Squamata, 5% Crocodilia, 0% Rhynchocephalia). Our review provides direction for the application of eDNA as an emerging tool in reptile ecology and conservation, especially when it can be paired with traditional monitoring approaches. Technologies associated with eDNA are rapidly advancing, and as techniques become more sensitive and accessible, we expect eDNA will be increasingly valuable for addressing key knowledge gaps for reptiles.
Collapse
Affiliation(s)
- Bethany Nordstrom
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Nicola Mitchell
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
| | - Margaret Byrne
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- Department of Biodiversity, Conservation and Attractions Biodiversity and Conservation Science Perth Western Australia Australia
| | - Simon Jarman
- School of Biological Sciences The University of Western Australia Crawley Western Australia Australia
- UWA Oceans Institute The University of Western Australia Crawley Western Australia Australia
| |
Collapse
|
8
|
Tercel MPTG, Moorhouse‐Gann RJ, Cuff JP, Drake LE, Cole NC, Goder M, Mootoocurpen R, Symondson WOC. DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink ( Leiolopisma telfairii). Ecol Evol 2022; 12:e8484. [PMID: 35127020 PMCID: PMC8794715 DOI: 10.1002/ece3.8484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/31/2021] [Accepted: 09/03/2021] [Indexed: 12/04/2022] Open
Abstract
Introduced species can exert disproportionately negative effects on island ecosystems, but their potential role as food for native consumers is poorly studied. Telfair's skinks are endemic omnivores living on Round Island, Mauritius, a globally significant site of biodiversity conservation. We aimed to determine the dietary diversity and key trophic interactions of Telfair's skinks, whether introduced species are frequently consumed, and if diet composition changes seasonally between male and female skinks. We used DNA metabarcoding of skink fecal samples to identify animals (COI) and plants (ITS2) consumed by skinks. There were 389 dietary presence counts belonging to 77 dietary taxa found across the 73 Telfair's skink fecal samples. Introduced taxa were cumulatively consumed more frequently than other categories, accounting for 49.4% of all detections, compared to cryptogenic (20.6%), native (20.6%), and endemic taxa (9.5%). The most frequently consumed introduced species was the ant, Pheidole megacephala, present in 40% of samples. Blue latan palm, Latania loddigesii, was the most frequently consumed endemic species, present in 33% of samples but was only detected in the dry season, when fruits are produced. We found a strong seasonal difference in diet composition explained by the presence of certain plant species solely or primarily in one season and a marked increase in the consumption of animal prey in the dry season. Male and female skinks consumed several taxa at different frequencies. These results present a valuable perspective on the role of introduced species in the trophic network of their invaded ecosystem. Both native and introduced species provide nutritional resources for skinks, and this may have management implications in the context of species conservation and island restoration.
Collapse
Affiliation(s)
| | - Rosemary J. Moorhouse‐Gann
- School of BiosciencesCardiff UniversityCardiffUK
- Durrell Wildlife Conservation TrustTrinityJersey
- Department of Animal & Plant SciencesNERC Biomolecular Analysis FacilitySheffieldUK
| | - Jordan P. Cuff
- School of BiosciencesCardiff UniversityCardiffUK
- Rothamsted Insect Survey, Rothamsted ResearchHarpendenUK
| | | | - Nik C. Cole
- Durrell Wildlife Conservation TrustTrinityJersey
- Mauritian Wildlife FoundationVacoasMauritius
| | | | | | | |
Collapse
|
9
|
Luo B, Xu R, Li Y, Zhou W, Wang W, Gao H, Wang Z, Deng Y, Liu Y, Feng J. Artificial light reduces foraging opportunities in wild least horseshoe bats. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 288:117765. [PMID: 34265558 DOI: 10.1016/j.envpol.2021.117765] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/06/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Artificial light at night has been proposed as a global threat to biodiversity. Insectivorous bats are strictly nocturnal animals that are vulnerable to disruption from artificial light. Given that many light-sensitive bats tend to avoid night light during roost departure, it is often assumed that nighttime light pollution reduces their foraging opportunities, albeit empirical evidence in support of this hypothesis remains elusive. Here, we used least horseshoe bats, Rhinolophus pusillus, to assess whether white artificial light is detrimental for the opportunities of foraging. We manipulated the levels of ambient illumination and perceived predation risk inside the bat roost. We monitored bats' emergence activity using high-speed video and audio recording systems. DNA-based faecal dietary analysis and insect survey were applied to determine activity time of prey in foraging areas. Following experimentally manipulation of white light-emitting diode (LED) lighting 0-15 min after sunset, bat pass, flight duration, and echolocation pulse emission decreased. The mean emergence time of bats flying out was delayed by 14 min under lit treatment compared with the dark control. Only 10% of bats left for foraging during 40 min of light exposure. Aversive effects of LED light on bat emergence were robust regardless of the presence of a potential predator. Insect prey reached a peak of abundance between 30 and 60 min after sunset. These results demonstrate that white artificial light hinders evening emergence behavior in least horseshoe bats, leading to a mismatch between foraging onset and peak food availability. Our findings highlight that light pollution overrides foraging onset, suggesting the importance of improving artificial lighting scheme near the roosts of light-sensitive bats.
Collapse
Affiliation(s)
- Bo Luo
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China; Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Rong Xu
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Yunchun Li
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Wenyu Zhou
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Weiwei Wang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China; Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Huimin Gao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China; Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Zhen Wang
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Yingchun Deng
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, 1# Shida Road, Nanchong, 637009, China
| | - Ying Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China; College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China.
| |
Collapse
|
10
|
Browett SS, Curran TG, O’Meara DB, Harrington AP, Sales NG, Antwis RE, O’Neill D, McDevitt AD. Primer biases in the molecular assessment of diet in multiple insectivorous mammals. Mamm Biol 2021. [DOI: 10.1007/s42991-021-00115-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractOur understanding of trophic interactions of small insectivorous mammals has been drastically improved with the advent of DNA metabarcoding. The technique has continued to be optimised over the years, with primer choice repeatedly being a vital factor for dietary inferences. However, the majority of dietary studies examining the effect of primer choice often rely on in silico analyses or comparing between species that occupy an identical niche type. Here, we apply DNA metabarcoding to empirically compare the prey detection capabilities of two widely used primer sets when assessing the diets of a flying (lesser horseshoe bat; Rhinolophus hipposideros) and two ground-dwelling insectivores (greater white-toothed shrew; Crocidura russula and pygmy shrew; Sorex minutus). Although R. hipposideros primarily rely on two prey orders (Lepidoptera and Diptera), the unique taxa detected by each primer shows that a combination of primers may be the best approach to fully describe bat trophic ecology. However, random forest classifier analysis suggests that one highly degenerate primer set detected the majority of both shrews’ diet despite higher levels of host amplification. The wide range of prey consumed by ground-dwelling insectivores can therefore be accurately documented from using a single broad-range primer set, which can decrease cost and labour. The results presented here show that dietary inferences will differ depending on the primer or primer combination used for insectivores occupying different niches (i.e., hunting in the air or ground) and demonstrate the importance of performing empirical pilot studies for novel study systems.
Collapse
|
11
|
Guo D, Ding J, Liu H, Zhou L, Feng J, Luo B, Liu Y. Social calls influence the foraging behavior in wild big-footed myotis. Front Zool 2021; 18:3. [PMID: 33413435 PMCID: PMC7791762 DOI: 10.1186/s12983-020-00384-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 12/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Why a variety of social animals emit foraging-associated calls during group foraging remains an open question. These vocalizations may be used to recruit conspecifics to food patches (i.e. food advertisement hypothesis) or defend food resources against competitors (food defence hypothesis), presumably depending on food availability. Insectivorous bats rely heavily on vocalizations for navigation, foraging, and social interactions. In this study, we used free-ranging big-footed myotis (Myotis macrodactylus Temminck, 1840) to test whether social calls produced in a foraging context serve to advertise food patches or to ward off food competitors. Using a combination of acoustic recordings, playback experiments with adult females and dietary monitoring (light trapping and DNA metabarcoding techniques), we investigated the relationship between insect availability and social vocalizations in foraging bats. RESULTS The big-footed myotis uttered low-frequency social calls composed of 7 syllable types during foraging interactions. Although the dietary composition of bats varied across different sampling periods, Diptera, Lepidoptera, and Trichoptera were the most common prey consumed. The number of social vocalizations was primarily predicted by insect abundance, insect species composition, and echolocation vocalizations from conspecifics. The number of conspecific echolocation pulses tended to decrease following the emission of most social calls. Feeding bats consistently decreased foraging attempts and food consumption during playbacks of social calls with distinctive structures compared to control trials. The duration of flight decreased 1.29-1.96 fold in the presence of social calls versus controls. CONCLUSIONS These results support the food defence hypothesis, suggesting that foraging bats employ social calls to engage in intraspecific food competition. This study provides correlative evidence for the role of insect abundance and diversity in influencing the emission of social calls in insectivorous bats. Our findings add to the current knowledge of the function of social calls in echolocating bats.
Collapse
Affiliation(s)
- Dongge Guo
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Jianan Ding
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Heng Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Lin Zhou
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, Changchun, 130118, China
| | - Bo Luo
- Key Laboratory of Southwest China Wildlife Resources Conservation of Ministry of Education, China West Normal University, Nanchong, 637002, China.
| | - Ying Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.
| |
Collapse
|
12
|
Tang K, Xie F, Liu H, Pu Y, Chen D, Qin B, Fu C, Wang Q, Chen S, Guo K. DNA metabarcoding provides insights into seasonal diet variations in Chinese mole shrew ( Anourosorex squamipes) with potential implications for evaluating crop impacts. Ecol Evol 2021; 11:376-389. [PMID: 33437436 PMCID: PMC7790647 DOI: 10.1002/ece3.7055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/11/2020] [Accepted: 10/25/2020] [Indexed: 01/02/2023] Open
Abstract
Diet analysis of potential small mammals pest species is important for understanding feeding ecology and evaluating their impact on crops and stored foods. Chinese mole shrew (Anourosorex squamipes), distributed in Southwest China, has previously been reported as a farmland pest. Effective population management of this species requires a better understanding of its diet, which can be difficult to determine with high taxonomic resolution using conventional microhistological methods. In this study, we used two DNA metabarcoding assays to identify 38 animal species and 65 plant genera from shrew stomach contents, which suggest that A. squamipes is an omnivorous generalist. Earthworms are the most prevalent (>90%) and abundant (>80%) food items in the diverse diet of A. squamipes. Species of the Fabaceae (frequency of occurrence [FO]: 88%; such as peanuts) and Poaceae (FO: 71%; such as rice) families were the most common plant foods identified in the diet of A. squamipes. Additionally, we found a seasonal decrease in the diversity and abundance of invertebrate foods from spring and summer to winter. Chinese mole shrew has a diverse and flexible diet throughout the year to adapt to seasonal variations in food availability, contributing to its survival even when food resources are limited. This study provides a higher resolution identification of the diet of A. squamipes than has been previously described and is valuable for understanding shrew feeding ecology as well as evaluating possible species impacts on crops.
Collapse
Affiliation(s)
- Ke‐yi Tang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Fei Xie
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Hong‐yi Liu
- College of Biology and the EnvironmentNanjing Forestry UniversityNanjingChina
| | - Ying‐ting Pu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Dan Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Bo‐xin Qin
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Chang‐kun Fu
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Qiong Wang
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Shun‐de Chen
- College of Life SciencesSichuan Normal UniversityChengduChina
| | - Ke‐ji Guo
- Central South Inventory and Planning Institute of National Forestry and Grassland AdministrationChangshaChina
| |
Collapse
|
13
|
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
|
14
|
Estimation of trophic niches in myrmecophagous spider predators. Sci Rep 2020; 10:8683. [PMID: 32457437 PMCID: PMC7250852 DOI: 10.1038/s41598-020-65623-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/09/2020] [Indexed: 11/21/2022] Open
Abstract
Among spiders, taxonomically the most diversified group of terrestrial predators, only a few species are stenophagous and feed on ants. The levels of stenophagy and ant-specialisation vary among such species. To investigate whether stenophagy is only a result of a local specialisation both fundamental and realised trophic niches need to be estimated. Here we investigated trophic niches in three closely-related spider species from the family Gnaphosidae (Callilepis nocturna, C. schuszteri, Nomisia exornata) with different levels of myrmecophagy. Acceptance experiments were used to estimate fundamental trophic niches and molecular methods to estimate realised trophic niches. For the latter two PCR primer sets were used as these can affect the niche breadth estimates. The general invertebrate ZBJ primers were not appropriate for detecting ant DNA as they revealed very few prey types, therefore ant-specific primers were used. The cut-off threshold for erroneous MOTUs was identified as 0.005% of the total number of valid sequences, at individual predator level it was 0.05%. The fundamental trophic niche of Callilepis species included mainly ants, while that of N. exornata included many different prey types. The realised trophic niche in Callilepis species was similar to its fundamental niche but in N. exornata the fundamental niche was wider than realised niche. The results show that Callilepis species are ant-eating (specialised) stenophagous predators, catching mainly Formicinae ants, while N. exornata is an ant-eating euryphagous predator catching mainly Myrmicinae ants.
Collapse
|
15
|
Supriya K, Price TD, Moreau CS. Competition with insectivorous ants as a contributor to low songbird diversity at low elevations in the eastern Himalaya. Ecol Evol 2020; 10:4280-4290. [PMID: 32489596 PMCID: PMC7246197 DOI: 10.1002/ece3.6196] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 02/21/2020] [Indexed: 01/03/2023] Open
Abstract
Competitive interactions between distantly related clades could cause complementary diversity patterns of these clades over large spatial scales. One such example might be ants and birds in the eastern Himalaya; ants are very common at low elevations but almost absent at mid-elevations where the abundance of other arthropods and insectivorous bird diversity peaks. Here, we ask if ants at low elevations could compete with birds for arthropod prey. Specifically, we studied the impact of the Asian weaver ant (Oecophylla smaragdina), a common aggressive ant at low elevations. Diet analysis using molecular methods demonstrate extensive diet overlap between weaver ants and songbirds at both low and mid-elevations. Trees without weaver ants have greater non-ant arthropod abundance and leaf damage. Experimental removal of weaver ants results in an increase in the abundance of non-ant arthropods. Notably, numbers of Coleoptera and Lepidoptera were most affected by removal experiments and were prominent components of both bird and weaver ant diets. Our results suggest that songbirds and weaver ants might potentially compete with each other for arthropod prey at low elevations, thereby contributing to lower insectivorous bird diversity at low elevations in eastern Himalaya. Competition with ants may shape vertebrate diversity patterns across broad biodiversity gradients.
Collapse
Affiliation(s)
- K. Supriya
- School of Life SciencesArizona State UniversityTempeAZUSA
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoILUSA
| | - Trevor D. Price
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoILUSA
- Department of Ecology and EvolutionUniversity of ChicagoChicagoILUSA
| | - Corrie S. Moreau
- Committee on Evolutionary BiologyUniversity of ChicagoChicagoILUSA
- Departments of Entomology and Ecology & Evolutionary BiologyCornell UniversityIthacaNYUSA
| |
Collapse
|
16
|
Browett SS, O'Meara DB, McDevitt AD. Genetic tools in the management of invasive mammals: recent trends and future perspectives. Mamm Rev 2020. [DOI: 10.1111/mam.12189] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samuel S. Browett
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| | - Denise B. O'Meara
- Molecular Ecology Research Group Eco‐Innovation Research Centre School of Science and Computing Waterford Institute of Technology Waterford Ireland
| | - Allan D. McDevitt
- Ecosystems and Environment Research Centre School of Science, Engineering and Environment University of Salford Salford M5 4WTUK
| |
Collapse
|
17
|
Food Spectrum of Common Kraits (Bungarus caeruleus): An Implication for Snakebite Prevention and Snake Conservation. J HERPETOL 2020. [DOI: 10.1670/18-054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
18
|
Zarzoso-Lacoste D, Bonnaud E, Corse E, Dubut V, Lorvelec O, De Meringo H, Santelli C, Meunier JY, Ghestemme T, Gouni A, Vidal E. Stuck amongst introduced species: Trophic ecology reveals complex relationships between the critically endangered Niau kingfisher and introduced predators, competitors and prey. NEOBIOTA 2019. [DOI: 10.3897/neobiota.53.35086] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The introduction of mammals on oceanic islands currently threatens or has caused the extinction of many endemic species. Cats and rats represent the major threat for 40 % of currently endangered island bird species. Direct (predation) and/or indirect (exploitative competition for food resource) trophic interactions are key mechanisms by which invaders cause the decrease or extinction of native populations. Here, we investigated both direct and indirect trophic interactions amongst four predator species (i.e. animals that hunt, kill and feed on other animals), including three introduced mammals (Felis silvestris catus, Rattus rattus and Rattus exulans) and one critically endangered native bird, the Niau kingfisher (Todiramphus gertrudae). All four species’ diets and prey availability were assessed from sampling at the six main kingfisher habitats on Niau Island during the breeding season. Diet analyses were conducted on 578 cat scats, 295 rat digestive tracts (218 R. exulans and 77 R. rattus) and 186 kingfisher pellets. Despite simultaneous use of morphological and PCR-based methods, no bird remains in cat and rat diet samples could be assigned to the Niau kingfisher, weakening the hypothesis of current intense predation pressure. However, we determined that Niau kingfishers mainly feed on introduced and/or cryptogenic prey and highlighted the potential for exploitative competition between this bird and both introduced rat species (for Dictyoptera, Coleoptera and Scincidae). We recommend removing the cats and both rat species, at least within kingfisher breeding and foraging areas (e.g. mechanical or chemical control, cat sterilisation, biosecurity reinforcement), to simultaneously decrease predation risk, increase key prey availability and boost kingfisher population dynamics.
Collapse
|
19
|
Garin I, Aihartza J, Goiti U, Arrizabalaga-Escudero A, Nogueras J, Ibáñez C. Bats from different foraging guilds prey upon the pine processionary moth. PeerJ 2019; 7:e7169. [PMID: 31316870 PMCID: PMC6613530 DOI: 10.7717/peerj.7169] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/22/2019] [Indexed: 11/30/2022] Open
Abstract
Outbreaks of the processionary moth Thaumetopoea pityocampa (Denis & Schiffermüller, 1775), a forest pest from the Palearctic, are thought to induce a behavioral response of bats, but up to now the moth has been seldom identified as bats’ prey. Studies on bat diets suggest moths with cyclical outbreaks attract a wide array of bat species from different foraging guilds. We test whether bats feed upon T. pityocampa in the Iberian Peninsula irrespective of the predator’s ecological and morphological features. We found that seven out of ten bat species belonging to different foraging guilds contained T. pityocampa DNA in their faeces and no difference was found in the foraging frequency among foraging guilds. A different size of the typical prey or the lack of fondness for moths can explain the absence of the pest in some bat species. Moreover, the intraspecific foraging frequency of T. pityocampa also changed with the sampling site likely representing differential availability of the moth. Lack of information on flight and dispersal behavior or the tympanate nature of the adult moth complicates understanding how different foraging guilds of bats prey upon the same prey. Our data suggests that T. pityocampa is a remarkable food source for many thousands of individual bats in the study area and we anticipate that more bats besides the species studied here are consuming this moth.
Collapse
Affiliation(s)
- Inazio Garin
- Zoologia eta Animali Zelulen Biologia Saila, UPV/EHU, Leioa, The Basque Country
| | - Joxerra Aihartza
- Zoologia eta Animali Zelulen Biologia Saila, UPV/EHU, Leioa, The Basque Country
| | - Urtzi Goiti
- Zoologia eta Animali Zelulen Biologia Saila, UPV/EHU, Leioa, The Basque Country
| | | | - Jesús Nogueras
- Evolutionary Ecology Department, Estación Biológica de Doñana, CSIC, Seville, Spain
| | - Carlos Ibáñez
- Evolutionary Ecology Department, Estación Biológica de Doñana, CSIC, Seville, Spain
| |
Collapse
|
20
|
Andriollo T, Gillet F, Michaux JR, Ruedi M. The menu varies with metabarcoding practices: A case study with the bat Plecotus auritus. PLoS One 2019; 14:e0219135. [PMID: 31276547 PMCID: PMC6611578 DOI: 10.1371/journal.pone.0219135] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/17/2019] [Indexed: 11/19/2022] Open
Abstract
Metabarcoding of feces has revolutionized the knowledge of animal diets by providing unprecedented resolution of consumed resources. However, it is still unclear how different methodological approaches influence the ecological conclusions that can be drawn from such data. Here, we propose a critical evaluation of several data treatments on the inferred diet of the bat Plecotus auritus using guano regularly collected from various colonies throughout the entire active season. First and unlike previous claims, our data indicates that DNA extracted from large amounts of fecal material issued from guano accumulates yield broader taxonomic diversity of prey than smaller numbers of pellets would do, provided that extraction buffer volumes are adapted to such increased amounts of material. Second, trophic niche analyses based on prey occurrence data uncover strong seasonality in the bat’s diet and major differences among neighboring maternity colonies. Third, while the removal of rare prey items is not always warranted as it introduces biases affecting particularly samples with greater prey species richness. Fourth, examination of distinct taxonomic depths in diet analyses highlights different aspects of food consumption providing a better understanding of the consumer’s diet. Finally, the biologically meaningful patterns recovered with presence-absence approaches are virtually lost when attempting to quantify prey consumed using relative read abundances. Even in an ideal situation where reference barcodes are available for most potential prey species, inferring realistic patterns of prey consumption remains relatively challenging. Although best practice in metabarcoding analyses will depend on the aims of the study, several previous methodological recommendations seem unwarranted for studying such diverse diets as that of brown long-eared bats.
Collapse
Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- Section of Biology, Faculty of Sciences, University of Geneva, Quai Ernest-Ansermet, Geneva, Switzerland
| | - François Gillet
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- Comportement et Écologie de la Faune Sauvage (CEFS), Institut National de la Recherche Agronomique, Auzeville, Castanet-Tolosan Cedex, France
| | - Johan R. Michaux
- Laboratoire de Génétique de la Conservation, Université de Liège, Institut de Botanique B22, Liège, Belgium
- CIRAD, Agirs Unit, TA C- 22/E- Campus international de Baillarguet, Montpellier Cedex, France
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, CP, CH, Geneva, Switzerland
- * E-mail:
| |
Collapse
|
21
|
Chang Y, Song S, Li A, Zhang Y, Li Z, Xiao Y, Jiang T, Feng J, Lin A. The roles of morphological traits, resource variation and resource partitioning associated with the dietary niche expansion in the fish-eating bat Myotis pilosus. Mol Ecol 2019; 28:2944-2954. [PMID: 31063664 DOI: 10.1111/mec.15127] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 04/27/2019] [Accepted: 04/29/2019] [Indexed: 12/29/2022]
Abstract
Niche expansion and shifts are involved in the response and adaptation to environmental changes. However, it is unclear how niche breadth evolves and changes toward higher-quality resources. Myotis pilosus is both an insectivore and a piscivore. We examined the dietary composition and seasonality in M. pilosus and the closely related Myotis fimbriatus using next-generation DNA sequencing. We tested whether resource variation or resource partitioning help explain the dietary expansion from insects to fish in M. pilosus. While diet composition and diversity varied significantly between summer and autumn, the proportion of fish-eating individuals did not significantly change between seasons in M. pilosus. Dietary overlap between M. pilosus and M. fimbriatus during the same seasons was much higher than within individual species across seasons. We recorded a larger body size, hind foot length, and body mass in M. pilosus than in M. fimbriatus and other insectivorous trawling bats from China. Similar morphological differences were found between worldwide fishing bats and nonfishing trawling bats. Our results suggest that variation in insect availability or interspecific competition may not play important roles in the dietary expansion from insects to fish in M. pilosus. Myotis pilosus has morphological advantages that may help it use fish as a diet component. The morphological advantage promoting dietary niche evolution toward higher quality resources may be more important than variation in the original resource and the effects of interspecific competition.
Collapse
Affiliation(s)
- Yang Chang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, China
| | - Shengjing Song
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Yu Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| | - Yanhong Xiao
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Tinglei Jiang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Key Laboratory of Vegetation Ecology of Education Ministry, Institute of Grassland Science, Northeast Normal University, Changchun, China.,College of Life Science, Jilin Agricultural University, Changchun, China
| | - Aiqing Lin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun, China.,Acoustic and Functional Ecology Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| |
Collapse
|
22
|
Littlefair JE, Zander A, Sena Costa C, Clare EL. DNA
metabarcoding reveals changes in the contents of carnivorous plants along an elevation gradient. Mol Ecol 2018; 28:281-292. [DOI: 10.1111/mec.14832] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 07/03/2018] [Accepted: 07/28/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Joanne E. Littlefair
- Department of Biology McGill University Montréal Québec Canada
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Axel Zander
- Department of Biology Unit of Ecology and Evolution University of Fribourg Fribourg Switzerland
| | - Clara Sena Costa
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences Queen Mary University of London London UK
| |
Collapse
|
23
|
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
|
24
|
Dunn JC, Stockdale JE, Moorhouse-Gann RJ, McCubbin A, Hipperson H, Morris AJ, Grice PV, Symondson WOC. The decline of the Turtle Dove: Dietary associations with body condition and competition with other columbids analysed using high-throughput sequencing. Mol Ecol 2018; 27:3386-3407. [PMID: 29927007 DOI: 10.1111/mec.14766] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/20/2017] [Indexed: 12/16/2022]
Abstract
Dietary changes linked to the availability of anthropogenic food resources can have complex implications for species and ecosystems, especially when species are in decline. Here, we use recently developed primers targeting the ITS2 region of plants to characterize diet from faecal samples of four UK columbids, with particular focus on the European turtle dove (Streptopelia turtur), a rapidly declining obligate granivore. We examine dietary overlap between species (potential competition), associations with body condition in turtle doves and spatiotemporal variation in diet. We identified 143 taxonomic units, of which we classified 55% to species, another 34% to genus and the remaining 11% to family. We found significant dietary overlap between all columbid species, with the highest between turtle doves and stock doves (Columba oenas), then between turtle doves and woodpigeons (Columba palumbus). The lowest overlap was between woodpigeons and collared doves (Streptopelia decaocto). We show considerable change in columbid diets compared to previous studies, probably reflecting opportunistic foraging behaviour by columbids within a highly anthropogenically modified landscape, although our data for nonturtle doves should be considered preliminary. Nestling turtle doves in better condition had a higher dietary proportion of taxonomic units from natural arable plant species and a lower proportion of taxonomic units from anthropogenic food resources such as garden bird seed mixes and brassicas. This suggests that breeding ground conservation strategies for turtle doves should include provision of anthropogenic seeds for adults early in the breeding season, coupled with habitat rich in accessible seeds from arable plants once chicks have hatched.
Collapse
Affiliation(s)
- Jenny C Dunn
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Bedfordshire, UK
- Cardiff School of Biosciences, Cardiff, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
- Joseph Banks Laboratories, School of Life Sciences, University of Lincoln, Lincoln, UK
| | | | | | | | - Helen Hipperson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Antony J Morris
- RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Bedfordshire, UK
| | | | | |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Arrizabalaga-Escudero A, Clare EL, Salsamendi E, Alberdi A, Garin I, Aihartza J, Goiti U. Assessing niche partitioning of co-occurring sibling bat species by DNA metabarcoding. Mol Ecol 2018; 27:1273-1283. [DOI: 10.1111/mec.14508] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Aitor Arrizabalaga-Escudero
- Department of Zoology and Animal Cell Biology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa The Basque Country Spain
- School of Biological and Chemical Sciences; Queen Mary University of London; London UK
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; London UK
| | - Egoitz Salsamendi
- Department of Zoology and Animal Cell Biology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa The Basque Country Spain
| | - Antton Alberdi
- Section for Evolutionary Genomics; Natural History Museum of Denmark; University of Copenhagen; Copenhagen Denmark
| | - Inazio Garin
- Department of Zoology and Animal Cell Biology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa The Basque Country Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa The Basque Country Spain
| | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology; Faculty of Science and Technology; University of the Basque Country UPV/EHU; Leioa The Basque Country Spain
| |
Collapse
|
27
|
Evolutionary Community Ecology: Time to Think Outside the (Taxonomic) Box. Trends Ecol Evol 2018; 33:240-250. [PMID: 29496340 DOI: 10.1016/j.tree.2018.01.014] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 01/30/2018] [Accepted: 01/30/2018] [Indexed: 11/23/2022]
Abstract
Ecologists and evolutionary biologists have long been interested in the role of interspecific competition in the diversification of clades. These studies often focus on a single taxonomic group, making the implicit assumption that important competitive interactions occur only between closely related taxa, despite abundant documentation of intense competition between species that are distantly related. Specifically, this assumption ignores convergence of distantly related competitors on limiting niche axes and thus may miss cryptic effects of distantly related competitors on the evolution of focal clades. For example, distantly related competitors may act as important drivers of niche conservatism within clades, a pattern commonly ascribed to evolutionary constraints or the abiotic environment. Here we propose an alternative model of how niche similarity evolves when the functional traits of interest are mediated by unrelated phenotypic traits, as is often the case for distantly related competitors. This model represents an important conceptual step towards a more accurate, taxonomically inclusive understanding of the role that competition plays in the micro- and macroevolution of interacting species.
Collapse
|
28
|
Toju H, Baba YG. DNA metabarcoding of spiders, insects, and springtails for exploring potential linkage between above- and below-ground food webs. ZOOLOGICAL LETTERS 2018; 4:4. [PMID: 29468086 PMCID: PMC5815251 DOI: 10.1186/s40851-018-0088-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Understanding feedback between above- and below-ground processes of biological communities is a key to the effective management of natural and agricultural ecosystems. However, as above- and below-ground food webs are often studied separately, our knowledge of material flow and community dynamics in terrestrial ecosystems remains limited. RESULTS We developed a high-throughput sequencing method for examining how spiders link above- and below-ground food webs as generalist predators. To overcome problems related to DNA-barcoding-based analyses of arthropod-arthropod interactions, we designed spider-specific blocking primers and Hexapoda-specific primers for the selective PCR amplification of Hexapoda prey sequences from spider samples. By applying the new DNA metabarcoding framework to spider samples collected in a temperate secondary forest in Japan, we explored the structure of a food web involving 15 spider species and various taxonomic groups of Hexapoda prey. These results support the hypothesis that multiple spider species in a community can prey on both above- and below-ground prey species, potentially coupling above- and below-ground food-web dynamics. CONCLUSIONS The PCR primers and metabarcoding pipeline described in this study are expected to accelerate nuclear marker-based analyses of food webs, illuminating poorly understood trophic interactions in ecosystems.
Collapse
Affiliation(s)
- Hirokazu Toju
- Center for Ecological Research, Kyoto University, Hirano 2-509-3, Otsu, Shiga 520-2113 Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency, Honcho 4-1-8, Kawaguchi, Saitama 332-0012 Japan
| | - Yuki G. Baba
- Institute for Agro-Environmental Sciences, NARO, Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604 Japan
| |
Collapse
|
29
|
Pearson CE, Symondson WOC, Clare EL, Ormerod SJ, Iparraguirre Bolaños E, Vaughan IP. The effects of pastoral intensification on the feeding interactions of generalist predators in streams. Mol Ecol 2017; 27:590-602. [PMID: 29219224 PMCID: PMC5887918 DOI: 10.1111/mec.14459] [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: 04/25/2017] [Revised: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 12/29/2022]
Abstract
Land‐use change can alter trophic interactions with wide‐ranging functional consequences, yet the consequences for aquatic food webs have been little studied. In part, this may reflect the challenges of resolving the diets of aquatic organisms using classical gut contents analysis, especially for soft‐bodied prey. We used next‐generation sequencing to resolve prey use in nearly 400 individuals of two predatory invertebrates (the Caddisfly, Rhyacophila dorsalis, and the Stonefly Dinocras cephalotes) in streams draining land with increasingly intensive livestock farming. Rhyacophila dorsalis occurred in all streams, whereas D. cephalotes was restricted to low intensities, allowing us to test whether: (i) apparent sensitivity to agriculture in the latter species reflects a more specialized diet and (ii) diet in R. dorsalis varied between sites with and without D. cephalotes. DNA was extracted from dissected gut contents, amplified without blocking probes and sequenced using Ion Torrent technology. Both predators were generalists, consuming 30 prey taxa with a preference for taxa that were abundant in all streams or that increased with intensification. Where both predators were present, their diets were nearly identical, and R. dorsalis's diet was virtually unchanged in the absence of D. cephalotes. The loss of D. cephalotes from more intensive sites was probably due to physicochemical stressors, such as sedimentation, rather than to dietary specialization, although wider biotic factors (e.g., competition with other predatory taxa) could not be excluded. This study provides a uniquely detailed description of predator diets along a land‐use intensity gradient, offering new insights into how anthropogenic stressors affect stream communities.
Collapse
Affiliation(s)
- C E Pearson
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - W O C Symondson
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - E L Clare
- School of Biological and Chemical Sciences, Queen Mary University, London, UK
| | - S J Ormerod
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| | - E Iparraguirre Bolaños
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK.,Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, Bilbao, Spain
| | - I P Vaughan
- Cardiff School of Biosciences, Cardiff University, Cardiff, UK
| |
Collapse
|
30
|
Doherty TS, Driscoll DA. Competition in the Historical Niche: A Response to Scheele et al. Trends Ecol Evol 2017; 33:147-148. [PMID: 29274664 DOI: 10.1016/j.tree.2017.12.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/01/2017] [Indexed: 11/24/2022]
Affiliation(s)
- Tim S Doherty
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Burwood Campus), Geelong, Australia.
| | - Don A Driscoll
- Deakin University, School of Life and Environmental Sciences, Centre for Integrative Ecology (Burwood Campus), Geelong, Australia
| |
Collapse
|
31
|
Cravens ZM, Brown VA, Divoll TJ, Boyles JG. Illuminating prey selection in an insectivorous bat community exposed to artificial light at night. J Appl Ecol 2017. [DOI: 10.1111/1365-2664.13036] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zachary M. Cravens
- Cooperative Wildlife Research Laboratory; Department of Zoology; Southern Illinois University; Carbondale IL USA
| | | | - Timothy J. Divoll
- Center for Bat Research, Outreach, and Conservation; Indiana State University; Terre Haute IN USA
| | - Justin G. Boyles
- Cooperative Wildlife Research Laboratory; Department of Zoology; Southern Illinois University; Carbondale IL USA
| |
Collapse
|
32
|
The diet of a nocturnal pelagic predator, the Bulwer's petrel, across the lunar cycle. Sci Rep 2017; 7:1384. [PMID: 28469170 PMCID: PMC5431196 DOI: 10.1038/s41598-017-01312-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 03/29/2017] [Indexed: 11/13/2022] Open
Abstract
The lunar cycle is believed to strongly influence the vertical distribution of many oceanic taxa, with implications for the foraging behaviour of nocturnal marine predators. Most studies to date testing lunar effects on foraging have focused on predator activity at-sea, with some birds and marine mammals demonstrating contrasting behavioural patterns, depending on the lunar-phase. However, to date no study has focused on how the lunar cycle might actually affect predator-prey interactions in the upper layers of the ocean. Here, we tested whether the diet of the predominantly nocturnal pelagic predator, the Bulwer’s petrel (Bulweria bulwerii) would change throughout the lunar cycle, using molecular analysis to augment detection and taxonomic resolution of prey collected from stomach-contents. We found no evidence of dietary shifts in species composition or diversity, with Bulwer’s petrel always consuming a wide range of mesopelagic species. Other co-variables potentially affecting light availability at-sea, such as percentage of cloud cover, did not confound our results. Moreover, many of the species found are thought not to reach the sea-surface. Our findings reveal that nocturnal predators are probably more specialized than previously assumed, irrespective of ambient-light, but also reveal deficiencies in our current understanding of species vertical distribution and predation-dynamics at-sea.
Collapse
|
33
|
Clare EL, Chain FJ, Littlefair JE, Cristescu ME. The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data. Genome 2016; 59:981-990. [DOI: 10.1139/gen-2015-0184] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The combination of DNA barcoding and high-throughput (next-generation) sequencing (metabarcoding) provides many promises but also serious challenges. Generating a reliable comparable estimate of biodiversity remains a central challenge to the application of the technology. Many approaches have been used to turn millions of sequences into distinct taxonomic units. However, the extent to which these methods impact the outcome of simple ecological analyses is not well understood. Here we performed a simple analysis of dietary overlap by skinks and shrews on Ile Aux Aigrettes, Mauritius. We used a combination of filtering thresholds and clustering algorithms on a COI metabarcoding dataset and demonstrate that all bioinformatics parameters will have interacting effects on molecular operational taxonomic unit (MOTU) recovery rates. These effects generated estimates covering two orders of magnitude. However, the effect on a simple ecological analysis was not large and, despite the wide variation in estimates of niche overlap, the same ecological conclusion was drawn in most cases. We advise that a conservative clustering programme coupled with larger sequence divergences to define a cluster, the removal of singletons, rigorous length filtering, and stringent match criteria for Molecular Identifier tags are preferable to avoid MOTU inflation and that the same parameters be used in all comparative analyses.
Collapse
Affiliation(s)
- Elizabeth L. Clare
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Frédéric J.J. Chain
- Department of Biology, McGill University, 1205 Docteur Penfield, Montréal, QC H3A 1B1, Canada
| | - Joanne E. Littlefair
- School of Biological and Chemical Sciences, Queen Mary University of London. Mile End Rd., London, E1 4NS, UK
| | - Melania E. Cristescu
- Department of Biology, McGill University, 1205 Docteur Penfield, Montréal, QC H3A 1B1, Canada
| |
Collapse
|
34
|
Salinas-Ramos VB, Herrera Montalvo LG, León-Regagnon V, Arrizabalaga-Escudero A, Clare EL. Dietary overlap and seasonality in three species of mormoopid bats from a tropical dry forest. Mol Ecol 2015; 24:5296-307. [DOI: 10.1111/mec.13386] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 08/27/2015] [Accepted: 09/10/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Valeria B. Salinas-Ramos
- Posgrado en Ciencias Biológicas, Instituto de Biología; Universidad Nacional Autónoma de México; México D. f. 04510 México
| | - L. Gerardo Herrera Montalvo
- Estación de Biología Chamela; Instituto de Biología; Universidad Nacional Autónoma de México; A.P. 21 San Patricio Jalisco 48980 México
| | - Virginia León-Regagnon
- Estación de Biología Chamela; Instituto de Biología; Universidad Nacional Autónoma de México; A.P. 21 San Patricio Jalisco 48980 México
| | - Aitor Arrizabalaga-Escudero
- Faculty of Science and Technology; University of the Basque Country UPV/EHU; Sarriena z/g Leioa E-48940 Spain
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile end Road London E1 4NS UK
| |
Collapse
|
35
|
Discovery of a monophagous true predator, a specialist termite-eating spider (Araneae: Ammoxenidae). Sci Rep 2015; 5:14013. [PMID: 26359085 PMCID: PMC4566138 DOI: 10.1038/srep14013] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 08/12/2015] [Indexed: 11/17/2022] Open
Abstract
True predators are characterised by capturing a number of prey items during their lifetime and by being generalists. Some true predators are facultative specialists, but very few species are stenophagous specialists that catch only a few closely related prey types. A monophagous true predator that would exploit a single prey species has not been discovered yet. Representatives of the spider family Ammoxenidae have been reported to have evolved to only catch termites. Here we tested the hypothesis that Ammoxenus amphalodes is a monophagous termite-eater capturing only Hodotermes mossambicus. We studied the trophic niche of A. amphalodes by means of molecular analysis of the gut contents using Next Generation Sequencing. We investigated their willingness to accept alternative prey and observed their specific predatory behaviour and prey capture efficiency. We found all of the 1.4 million sequences were H. mossambicus. In the laboratory A. amphalodes did not accept any other prey, including other termite species. The spiders attacked the lateral side of the thorax of termites and immobilised them within 1 min. The paralysis efficiency was independent of predator:prey size ratio. The results strongly indicate that A. amphalodes is a monophagous prey specialist, specifically adapted to feed on H. mossambicus.
Collapse
|
36
|
King RA, Symondson WOC, Thomas RJ. Molecular analysis of faecal samples from birds to identify potential crop pests and useful biocontrol agents in natural areas. BULLETIN OF ENTOMOLOGICAL RESEARCH 2015; 105:261-272. [PMID: 25572526 DOI: 10.1017/s0007485314000935] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Wild habitats adjoining farmland are potentially valuable sources of natural enemies, but also of pests. Here we tested the utility of birds as 'sampling devices', to identify the diversity of prey available to predators and particularly to screen for pests and natural enemies using natural ecosystems as refugia. Here we used PCR to amplify prey DNA from three sympatric songbirds foraging on small invertebrates in Phragmites reedbed ecosystems, namely the Reed Warbler (Acrocephalus scirpaceus), Sedge Warbler (Acrocephalus schoenobaenus) and Cetti's Warbler (Cettia cetti). A recently described general invertebrate primer pair was used for the first time to analyse diets. Amplicons were cloned and sequenced, then identified by reference to the Barcoding of Life Database and to our own sequences obtained from fresh invertebrates. Forty-five distinct prey DNA sequences were obtained from 11 faecal samples, of which 39 could be identified to species or genus. Targeting three warbler species ensured that species-specific differences in prey choice broadened the range of prey taken. Amongst the prey found in reedbeds were major pests (including the tomato moth Lacanobia oleracea) as well as many potentially valuable natural enemies including aphidophagous hoverflies and braconid wasps. Given the mobility of birds, this approach provides a practical way of sampling a whole habitat at once, providing growers with information on possible invasion by locally resident pests and the colonization potential of natural enemies from local natural habitats.
Collapse
Affiliation(s)
- R A King
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - W O C Symondson
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| | - R J Thomas
- Cardiff School of Biosciences,The Sir Martin Evans Building,Cardiff University,Museum Avenue,Cardiff CF10 3AX,UK
| |
Collapse
|
37
|
Lawson Handley L. How will the ‘molecular revolution’ contribute to biological recording? Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12516] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lori Lawson Handley
- Evolutionary Biology Group; School of Biological, Biomedical and Environmental Sciences; University of Hull; Cottingham Road Hull HU6 7RX UK
| |
Collapse
|
38
|
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
|
39
|
Symondson WOC, Harwood JD. Special issue on molecular detection of trophic interactions: unpicking the tangled bank. Introduction. Mol Ecol 2014; 23:3601-4. [PMID: 25051891 DOI: 10.1111/mec.12831] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 06/06/2014] [Indexed: 01/27/2023]
Affiliation(s)
- William O C Symondson
- Cardiff School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | | |
Collapse
|
40
|
Sedlock JL, Krüger F, Clare EL. Island bat diets: does it matter more who you are or where you live? Mol Ecol 2014; 23:3684-94. [DOI: 10.1111/mec.12732] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 02/21/2014] [Accepted: 03/05/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Jodi L. Sedlock
- Biology Department; Lawrence University; 711 E. Boldt Way Appleton WI 54911 USA
| | - Frauke Krüger
- Institute of Natural Resource Conservation; University of Kiel; Olshausenstr. 75 24118 Kiel Germany
| | - Elizabeth L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| |
Collapse
|
41
|
Krüger F, Clare EL, Symondson WOC, Keišs O, Pētersons G. Diet of the insectivorous bat Pipistrellus nathusii during autumn migration and summer residence. Mol Ecol 2013; 23:3672-83. [PMID: 24118366 DOI: 10.1111/mec.12547] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/10/2013] [Accepted: 09/13/2013] [Indexed: 11/29/2022]
Abstract
Migration is widespread among vertebrates, yet bat migration has received little attention and only in the recent decades has a better understanding of it been gained. Migration can cause significant changes in behaviour and physiology, due to increasing energy demands and aerodynamic constraints. Dietary shifts, for example, have been shown to occur in birds before onset of migration. For bats, it is not known if a change in diet occurs during migration, although breeding season-related dietary preference has been documented. It is known that a diet rich in fats and the accumulation of fat deposits do increase the flight range of migratory bats. Some bat species can be regarded as long-distance migrants, covering up to 2000 km between summer and winter roosting areas. Pipistrellus nathusii (Vespertilionidae), a European long-distant migrant, travels each year along the Baltic Sea from north-eastern Europe to hibernate in central and southern Europe. This study presents data on the dietary habits of migrating Pipistrellus nathusii compared with those during the breeding season. We analysed faecal samples from bats on fall migration caught at the Ornithological Field Station in Pape, Latvia and from samples collected in North-Latvian summer roosts. We applied both morphological identification and molecular methods, as morphological methods also recognize life stages of prey and can contribute frequency data. The diets of bats on migration and breeding bats were similar, with Diptera and Lepidoptera comprising the major prey categories. However, certain prey groups could be explained by the different hunting habitats exploited during migration vs. summer residence.
Collapse
Affiliation(s)
- Frauke Krüger
- Institute of Natural Resource Conservation, University of Kiel, Olshausenstr. 75, 24118, Kiel, Germany; Echolot Gbr, Eulerstr. 12, 48155, Münster, Germany
| | | | | | | | | |
Collapse
|
42
|
Clare EL, Symondson WOC, Broders H, Fabianek F, Fraser EE, MacKenzie A, Boughen A, Hamilton R, Willis CKR, Martinez-Nuñez F, Menzies AK, Norquay KJO, Brigham M, Poissant J, Rintoul J, Barclay RMR, Reimer JP. The diet ofMyotis lucifugusacross Canada: assessing foraging quality and diet variability. Mol Ecol 2013; 23:3618-32. [DOI: 10.1111/mec.12542] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2013] [Revised: 09/11/2013] [Accepted: 09/13/2013] [Indexed: 01/16/2023]
Affiliation(s)
- Elizabeth L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - William O. C. Symondson
- Cardiff School of Biosciences; Cardiff University; The Sir Martin Evans Building, Museum Avenue Cardiff CF10 3AX UK
| | - Hugh Broders
- Department of Biology; Saint Mary's University; Robie Street Halifax Nova Scotia Canada B3H 3C3
| | - François Fabianek
- Faculty of Forestry, Geography and Geomatics; Laval University; 2405 rue de la Terrasse Quebec Canada G1V 0A6
| | - Erin E. Fraser
- Environmental Science (Biology); Memorial University of Newfoundland Grenfell Campus; 20 University Dr. Corner Brook Newfoundland and Labrador Canada A2H 5G4
| | - Alistair MacKenzie
- Pinery Provincial Park; Ontario Parks; 9526 Lakeshore Road, R.R. #2 Grand Bend Ontario Canada N0M 1T0
| | - Andrew Boughen
- Lake St. George Conservation Field Centre; Toronto and Region Conservation; 950 Bethesda Sd. Rd. Richmond Hill Ontario Canada L4E 3G2
| | - Rachel Hamilton
- Department of Biology, Biological and Geological Sciences Building; University of Western Ontario; London Ontario Canada N6A 5B7
| | - Craig K. R. Willis
- Department of Biology; University of Winnipeg; 515 Portage Ave. Winnipeg Manitoba Canada R3B 2E9
| | - Felix Martinez-Nuñez
- Department of Biology; University of Winnipeg; 515 Portage Ave. Winnipeg Manitoba Canada R3B 2E9
| | - Allyson K. Menzies
- Department of Biology; University of Winnipeg; 515 Portage Ave. Winnipeg Manitoba Canada R3B 2E9
| | - Kaleigh J. O. Norquay
- Department of Biology; University of Winnipeg; 515 Portage Ave. Winnipeg Manitoba Canada R3B 2E9
| | - Mark Brigham
- Department of Biology, Laboratory Building; University of Regina; Wascana Parkway Regina Saskatchewan Canada S4S 0A2
| | - Joseph Poissant
- Department of Biology, Laboratory Building; University of Regina; Wascana Parkway Regina Saskatchewan Canada S4S 0A2
| | - Jody Rintoul
- Department of Biology, Laboratory Building; University of Regina; Wascana Parkway Regina Saskatchewan Canada S4S 0A2
| | - Robert M. R. Barclay
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W. Calgary Alberta Canada T2N 1N4
| | - Jesika P. Reimer
- Department of Biological Sciences; University of Calgary; 2500 University Drive N.W. Calgary Alberta Canada T2N 1N4
| |
Collapse
|
43
|
Burgar JM, Murray DC, Craig MD, Haile J, Houston J, Stokes V, Bunce M. Who's for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed. Mol Ecol 2013; 23:3605-17. [PMID: 24118181 DOI: 10.1111/mec.12531] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 09/05/2013] [Accepted: 09/13/2013] [Indexed: 02/04/2023]
Abstract
Effective management and conservation of biodiversity requires understanding of predator-prey relationships to ensure the continued existence of both predator and prey populations. Gathering dietary data from predatory species, such as insectivorous bats, often presents logistical challenges, further exacerbated in biodiversity hot spots because prey items are highly speciose, yet their taxonomy is largely undescribed. We used high-throughput sequencing (HTS) and bioinformatic analyses to phylogenetically group DNA sequences into molecular operational taxonomic units (MOTUs) to examine predator-prey dynamics of three sympatric insectivorous bat species in the biodiversity hotspot of south-western Australia. We could only assign between 4% and 20% of MOTUs to known genera or species, depending on the method used, underscoring the importance of examining dietary diversity irrespective of taxonomic knowledge in areas lacking a comprehensive genetic reference database. MOTU analysis confirmed that resource partitioning occurred, with dietary divergence positively related to the ecomorphological divergence of the three bat species. We predicted that bat species' diets would converge during times of high energetic requirements, that is, the maternity season for females and the mating season for males. There was an interactive effect of season on female, but not male, bat species' diets, although small sample sizes may have limited our findings. Contrary to our predictions, females of two ecomorphologically similar species showed dietary convergence during the mating season rather than the maternity season. HTS-based approaches can help elucidate complex predator-prey relationships in highly speciose regions, which should facilitate the conservation of biodiversity in genetically uncharacterized areas, such as biodiversity hotspots.
Collapse
Affiliation(s)
- Joanna M Burgar
- School of Veterinary and Life Sciences, Murdoch University, 90 South Street, Murdoch, WA, 6150, Australia
| | | | | | | | | | | | | |
Collapse
|
44
|
Clare EL, Symondson WOC, Fenton MB. An inordinate fondness for beetles? Variation in seasonal dietary preferences of night-roosting big brown bats (Eptesicus fuscus). Mol Ecol 2013; 23:3633-47. [DOI: 10.1111/mec.12519] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Elizabeth L. Clare
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
| | - William O. C. Symondson
- Cardiff School of Biosciences; The Sir Martin Evans Building, Museum Avenue Cardiff CF10 3AX UK
| | | |
Collapse
|