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Haarsma AJ, Jongejans E, Duijm E, van der Graaf C, Lammers Y, Sharma M, Siepel H, Gravendeel B. Female pond bats hunt in other areas than males and consume lighter prey when pregnant. J Mammal 2023; 104:1191-1204. [PMID: 38059006 PMCID: PMC10697422 DOI: 10.1093/jmammal/gyad096] [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: 11/30/2022] [Accepted: 09/07/2023] [Indexed: 12/08/2023] Open
Abstract
Animals with large energy requirements are forced to optimize their hunting strategy, which may result in differentiation of the diet between sexes and across seasons. Here, we examined spatiotemporal variation in the diet of both sexes of the Pond Bat Myotis dasycneme, a species known to have spatial segregation of sexes when the young are born and lactating. Fecal pellets were collected from live animals for a period of 15 years at various locations in the Netherlands. A total of 535 pellets were successfully analyzed by microscopy and an additional 160 pellets by DNA metabarcoding. Morphological and molecular analyses showed that the diet of pregnant and lactating pond bats differed significantly from the diet of females with no reproductive investment. Further analyses of the data showed that pregnant female pond bats are highly dependent on small prey and pupae, mainly nonbiting midges and mosquitoes (Diptera: Chironomidae and Culicidae). These insects can be found in large quantities in peatlands intersected with shallow waterways, the habitat type in which female pond bats were observed more often than males. Our results suggest that during pregnancy the spatial segregation of sexes coincides with sex-specific diets, which might reflect habitat selection based on energy requirements, in addition to lowered intraspecific competition.
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Affiliation(s)
- Anne-Jifke Haarsma
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Eelke Jongejans
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Netherlands Institute of Ecology, Department of Animal Ecology, Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Elza Duijm
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Carolien van der Graaf
- Bat Research Consultancy Vroegvlieger, Ellekomstraat 70, 2573 XG Den Haag, The Netherlands
| | - Youri Lammers
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
| | - Milan Sharma
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
- HZ University of Applied Sciences, Life Sciences cluster, Edisonweg 4, 4382 NW Vlissingen, The Netherlands
| | - Henk Siepel
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Barbara Gravendeel
- Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
- Naturalis Biodiversity Center, Evolutionary Ecology Group, Darwinweg 2, 2333 CR Leiden, The Netherlands
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Esnaola A, Larrañaga A, González-Esteban J, Elosegi A, Aihartza J. Using biological traits to assess diet selection: the case of the Pyrenean Desman. J Mammal 2023; 104:1205-1215. [PMID: 38059010 PMCID: PMC10697428 DOI: 10.1093/jmammal/gyad061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/13/2023] [Indexed: 12/08/2023] Open
Abstract
Traditionally, researchers have assessed diet selection by comparing consumed versus available taxa. However, taxonomic assignment is probably irrelevant for predators, who likely base their selection on characteristics including prey size, habitat, or behavior. Here, we use an aquatic insectivore, the threatened Pyrenean Desman (Galemys pyrenaicus), as a model species to assess whether biological traits help unravel the criteria driving food and habitat preferences. We reanalyzed data from a previous taxonomy-based study of prey selection in two contrasting streams, one with excellent conservation status and the other affected by diversion for hydropower and forestry. Available and consumed prey were characterized according to nine biological traits, and diet selection was estimated by comparing availability-measured from Surber net samples, and consumption-analyzed by metabarcoding desman feces. Traits offered a biologically coherent image of diet and almost identical selection patterns in both streams, depicting a highly specialized rheophilic predator. Desmans positively selected prey with a preference for fast flow and boulder substrate, indicating their preferred riffle habitat. On the other hand, they positively selected prey with larger but not the largest potential size, living in the water column or the litter, and not inside sediments. They also chose agile prey, swimmers or prey attached to the substrate, prey with high body flexibility, and prey living exposed and clustered in groups. Overall, our results offer a picture of desman diet preference and point to biological traits as being better than taxonomic identity to describe the diet preference of consumers.
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Affiliation(s)
- Amaiur Esnaola
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, the Basque Country 48940, Spain
- EKOLUR Asesoría Ambiental – Ingurumen Aholkularitza S.L.L., Oiartzun, the Basque Country 20180, Spain
| | - Aitor Larrañaga
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, Leioa, the Basque Country 48940, Spain
| | | | - Arturo Elosegi
- Department of Plant Biology and Ecology, University of the Basque Country UPV/EHU, Leioa, the Basque Country 48940, Spain
| | - Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Leioa, the Basque Country 48940, Spain
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3
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Aihartza J, Vallejo N, Aldasoro M, García-Mudarra JL, Goiti U, Nogueras J, Ibáñez C. Aerospace-foraging bats eat seasonably across varying habitats. Sci Rep 2023; 13:19576. [PMID: 37950015 PMCID: PMC10638376 DOI: 10.1038/s41598-023-46939-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Recent research has confirmed the efficiency of insectivorous bats as pest suppressors, underlining the ecological services they offer in agroecosystems. Therefore, some efforts try to enhance bat foraging in agricultural landscapes by acting upon environmental factors favouring them. In this study, we monitored a Miniopterus schreibersii colony, in the southern Iberian Peninsula. We intensively sampled their faeces and analysed them by metabarcoding to describe how the bent-winged bat diet would change with time, and to test whether their most-consumed prey would seasonally depend on different landscapes or habitats. Our results confirm that M. schreibersii are selective opportunist predators of moths, dipterans, mayflies, and other fluttering insects, shifting their diet to temporary peaks of prey availability in their foraging range, including both pest and non-pest insects. Supporting our hypothesis, throughout the year, M. schreibersii consume insects linked to diverse open habitats, including wetlands, grassland, diverse croplands, and woodland. The importance of each prey habitat varies seasonally, depending on their insect phenology, making bats indirectly dependent on a diverse landscape as their primary prey source. Bats' predation upon pest insects is quantitatively high, consuming around 1610 kg in 5 months, of which 1467 kg correspond to ten species. So, their suppression effect may be relevant, mainly in patchy heterogeneous landscapes, where bats' foraging may concentrate in successive outbursts of pests, affecting different crops or woodlands. Our results stress that to take advantage of the ecosystem services of bats or other generalist insectivores, keeping the environmental conditions they require to thrive, particularly a heterogeneous landscape within the colony's foraging area, is crucial.
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Affiliation(s)
- Joxerra Aihartza
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain.
| | - Nerea Vallejo
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | - Miren Aldasoro
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | | | - Urtzi Goiti
- Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Sarriena s/n, 48940, Leioa, The Basque Country, Spain
| | - Jesus Nogueras
- Estación Biológica de Doñana (CSIC), P.O. Box 1056, 41080, Sevilla, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), P.O. Box 1056, 41080, Sevilla, Spain
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de Framond L, Beleyur T, Lewanzik D, Goerlitz HR. Calibrated microphone array recordings reveal that a gleaning bat emits low-intensity echolocation calls even in open-space habitat. J Exp Biol 2023; 226:jeb245801. [PMID: 37655585 PMCID: PMC10560550 DOI: 10.1242/jeb.245801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
Echolocating bats use ultrasound for orientation and prey capture in darkness. Ultrasound is strongly attenuated in air. Consequently, aerial-hawking bats generally emit very intense echolocation calls to maximize detection range. However, call levels vary more than tenfold (>20 dB) between species and are tightly linked to the foraging strategy. The brown long-eared bat (Plecotus auritus) is a primarily gleaning, low-amplitude species that may occasionally hawk airborne prey. We used state-of-the-art calibrated acoustic 3D-localization and automated call analysis to measure P. auritus' source levels. Plecotus auritus emits echolocation calls of low amplitude (92 dB rmsSPL re. 20 µPa at 10 cm) even while flying in open-space. While P. auritus thus probably benefits from delayed evasive manoeuvres of eared insects, we propose that low-amplitude echolocation did not evolve as an adaptive countermeasure, but is limited by morphological constraints.
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Affiliation(s)
- Léna de Framond
- Acoustic and Functional Ecology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Thejasvi Beleyur
- Acoustic and Functional Ecology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
- Department of Biology, University of Konstanz, 78464 Konstanz, Germany
- Centre for the Advanced Study of Collective Behaviour, University of Konstanz, 78464 Konstanz, Germany
| | - Daniel Lewanzik
- Acoustic and Functional Ecology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Holger R. Goerlitz
- Acoustic and Functional Ecology, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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Ancillotto L, Falanga A, Agostinetto G, Tommasi N, Garonna AP, de Benedetta F, Bernardo U, Galimberti A, Conti P, Russo D. Predator-prey traits and foraging habitat shape the diet of a common insectivorous bat. ACTA OECOLOGICA 2023. [DOI: 10.1016/j.actao.2023.103890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Andreas M, Naďo L, Bendová B, Uhrin M, Maxinová E, Lučan R, Benda P. Trophic niche and diet composition of the northernmost population of the Mediterranean horseshoe bat (Rhinolophus euryale) with conservation implications. MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00674-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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7
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Hemprich-Bennett DR, Kemp VA, Blackman J, Lewis OT, Struebig MJ, Bernard H, Kratina P, Rossiter SJ, Clare EL. Selective Logging Shows No Impact on the Dietary Breadth of a Generalist Bat Species: The Fawn Leaf-Nosed Bat (Hipposideros cervinus). Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.750269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Logging activities degrade forest habitats across large areas of the tropics, but the impacts on trophic interactions that underpin forest ecosystems are poorly understood. DNA metabarcoding provides an invaluable tool to investigate such interactions, allowing analysis at a far greater scale and resolution than has previously been possible. We analysed the diet of the insectivorous fawn leaf-nosed bat Hipposideros cervinus across a forest disturbance gradient in Borneo, using a dataset of ecological interactions from an unprecedented number of bat-derived faecal samples. Bats predominantly consumed insects from the orders Lepidoptera, Diptera, Blattodea, and Coleoptera, and the taxonomic composition of their diet remained relatively consistent across sites regardless of logging disturbance. There was little difference in the richness of prey consumed per-bat in each logging treatment, indicating potential resilience of this species to habitat degradation. In fact, bats consumed a high richness of prey items, and intensive sampling is needed to reliably compare feeding ecology over multiple sites. Multiple bioinformatic parameters were used, to assess how they altered our perception of sampling completeness. While parameter choice altered estimates of completeness, a very high sampling effort was always required to detect the entire prey community.
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8
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Harnessing the Power of Metabarcoding in the Ecological Interpretation of Plant-Pollinator DNA Data: Strategies and Consequences of Filtering Approaches. DIVERSITY 2021. [DOI: 10.3390/d13090437] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Although DNA metabarcoding of pollen mixtures has been increasingly used in the field of pollination biology, methodological and interpretation issues arise due to its high sensitivity. Filtering or maintaining false positives, contaminants, and rare taxa or molecular features could lead to different ecological results. Here, we reviewed how this choice has been addressed in 43 studies featuring pollen DNA metabarcoding, which highlighted a very high heterogeneity of filtering methods. We assessed how these strategies shaped pollen assemblage composition, species richness, and interaction networks. To do so, we compared four processing methods: unfiltering, filtering with a proportional 1% of sample reads, a fixed threshold of 100 reads, and the ROC approach (Receiver Operator Characteristic). The results indicated that filtering impacted species composition and reduced species richness, with ROC emerging as a conservative approach. Moreover, in contrast to unfiltered networks, filtering decreased network Connectance and Entropy, and it increased Modularity and Connectivity, indicating that using cut-off thresholds better describes interactions. Overall, unfiltering might compromise reliable ecological interpretations, unless a study targets rare species. We discuss the suitability of each filtering type, plead for justifying filtering strategies on biological or methodological bases and for developing shared approaches to make future studies more comparable.
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9
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Andriollo T, Michaux JR, Ruedi M. Food for everyone: Differential feeding habits of cryptic bat species inferred from DNA metabarcoding. Mol Ecol 2021; 30:4584-4600. [PMID: 34245618 PMCID: PMC8518853 DOI: 10.1111/mec.16073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/07/2021] [Accepted: 07/08/2021] [Indexed: 11/29/2022]
Abstract
Ecological theory postulates that niches of co‐occurring species must differ along some ecological dimensions in order to allow their stable coexistence. Yet, many biological systems challenge this competitive exclusion principle. Insectivorous bats from the Northern Hemisphere typically form local assemblages of multiple species sharing highly similar functional traits and pertaining to identical feeding guilds. Although their trophic niche can be accessed with unprecedented details using genetic identification of prey, the underlying mechanisms of resource partitioning remain vastly unexplored. Here, we studied the differential diet of three closely‐related bat species of the genus Plecotus in sympatry and throughout their entire breeding season using DNA metabarcoding. Even at such a small geographic scale, we identified strong seasonal and spatial variation of their diet composition at both intra‐ and interspecific levels. Indeed, while the different bats fed on a distinct array of prey during spring, they showed higher trophic niche overlap during summer and fall, when all three species switched their hunting behaviour to feed on few temporarily abundant moths. By recovering 19 ecological traits for over 600 prey species, we further inferred that each bat species used different feeding grounds and hunting techniques, suggesting that niche partitioning was primarily habitat‐driven. The two most‐closely related bat species exhibited very distinct foraging habitat preferences, while the third, more distantly‐related species was more generalist. These results highlight the need of temporally comprehensive samples to fully understand species coexistence, and that valuable information can be derived from the taxonomic identity of prey obtained by metabarcoding approaches.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, Switzerland.,Section of Biology, Faculty of Sciences, University of Geneva, Geneva, Switzerland
| | - 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 5, France
| | - Manuel Ruedi
- Department of Mammalogy and Ornithology, Natural History Museum of Geneva, Geneva, Switzerland
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10
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Using next generation sequencing of alpine plants to improve fecal metabarcoding diet analysis for Dall's sheep. BMC Res Notes 2021; 14:173. [PMID: 33962681 PMCID: PMC8103577 DOI: 10.1186/s13104-021-05590-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
Objectives Dall’s sheep (Ovis dalli dalli) are important herbivores in the mountainous ecosystems of northwestern North America, and recent declines in some populations have sparked concern. Our aim was to improve capabilities for fecal metabarcoding diet analysis of Dall’s sheep and other herbivores by contributing new sequence data for arctic and alpine plants. This expanded reference library will provide critical reference sequence data that will facilitate metabarcoding diet analysis of Dall’s sheep and thus improve understanding of plant-animal interactions in a region undergoing rapid climate change. Data description We provide sequences for the chloroplast rbcL gene of 16 arctic-alpine vascular plant species that are known to comprise the diet of Dall’s sheep. These sequences contribute to a growing reference library that can be used in diet studies of arctic herbivores. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05590-z.
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11
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Prey partitioning between sympatric wild carnivores revealed by DNA metabarcoding: a case study on wolf (Canis lupus) and coyote (Canis latrans) in northeastern Washington. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01337-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Subrata SA, Siregar SRT, André A, Michaux JR. Identifying prey of the Javan mongoose (Urva javanica) in Java from fecal samples using next-generation sequencing. Mamm Biol 2020. [DOI: 10.1007/s42991-020-00086-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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13
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Hemprich-Bennett DR, Oliveira HFM, Le Comber SC, Rossiter SJ, Clare EL. Assessing the impact of taxon resolution on network structure. Ecology 2020; 102:e03256. [PMID: 33226629 DOI: 10.1002/ecy.3256] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/01/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023]
Abstract
Constructing ecological networks has become an indispensable approach in understanding how different taxa interact. However, the methods used to generate data in network research vary widely among studies, potentially limiting our ability to compare results meaningfully. In particular, methods of classifying nodes vary in their precision, likely altering the architecture of the network studied. For example, rather than being classified as Linnaean species, taxa are regularly assigned to morphospecies in observational studies, or to molecular operational taxonomic units (MOTUs) in molecular studies, with the latter defined based on an arbitrary threshold of sequence similarity. Although the use of MOTUs in ecological networks holds great potential, especially for allowing rapid construction of large data sets of interactions, it is unclear how the choice of clustering threshold can influence the conclusions obtained. To test the impact of taxonomic precision on network architecture, we obtained and analyzed 16 data sets of ecological interactions, inferred from metabarcoding and observations. Our comparisons of networks constructed under a range of sequence thresholds for assigning taxa demonstrate that even small changes in node resolution can cause wide variation in almost all key metric values. Moreover, relative values of commonly used metrics such as robustness were seen to fluctuate continuously with node resolution, thereby potentially causing error in conclusions drawn when comparing multiple networks. In observational networks, we found that changing node resolution could, in some cases, lead to substantial changes to measurements of network topology. Overall, our findings highlight the importance of classifying nodes to the greatest precision possible, and demonstrate the need for caution when comparing networks that differ with respect to node resolution, even where taxonomic groups and interaction types are similar. In such cases, we recommend that comparisons of networks should focus on relative differences rather than absolute values between the networks studied.
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Affiliation(s)
- David R Hemprich-Bennett
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK.,Department of Zoology, Zoology Research and Administration Building, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Hernani F M Oliveira
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Steven C Le Comber
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Stephen J Rossiter
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
| | - Elizabeth L Clare
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London, E1 4NS, UK
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14
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Tournayre O, Leuchtmann M, Filippi‐Codaccioni O, Trillat M, Piry S, Pontier D, Charbonnel N, Galan M. In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses. Ecol Evol 2020; 10:6310-6332. [PMID: 32724515 PMCID: PMC7381572 DOI: 10.1002/ece3.6362] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/20/2020] [Accepted: 04/22/2020] [Indexed: 12/28/2022] Open
Abstract
During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.
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Affiliation(s)
- Orianne Tournayre
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | | | - Ondine Filippi‐Codaccioni
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Marine Trillat
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Sylvain Piry
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Dominique Pontier
- LabEx ECOFECT “Ecoevolutionary Dynamics of Infectious DiseasesUniversité de LyonLyonFrance
- CNRSLaboratoire de Biométrie et Biologie ÉvolutiveUMR5558Université de LyonUniversité Lyon 1VilleurbanneFrance
| | - Nathalie Charbonnel
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
| | - Maxime Galan
- CBGPINRAECIRADIRDMontpellier SupAgroUniversité de MontpellierMontpellierFrance
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15
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French BJ, Lim YW, Zgliczynski BJ, Edwards RA, Rohwer F, Sandin SA. Decoding diversity in a coral reef fish species complex with restricted range using metagenomic sequencing of gut contents. Ecol Evol 2020; 10:3413-3423. [PMID: 32273998 PMCID: PMC7141070 DOI: 10.1002/ece3.6138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/22/2020] [Accepted: 02/03/2020] [Indexed: 12/21/2022] Open
Abstract
AIM Identification of the processes that generate and maintain species diversity within the same region can provide insight into biogeographic patterns at broader spatiotemporal scales. Hawkfishes in the genus Paracirrhites are a unique taxon to explore with respect to niche differentiation, exhibiting diagnostic differences in coloration, and an apparent center of distribution outside of the Indo-Malay-Philippine (IMP) biodiversity hotspot for coral reef fishes. Our aim is to use next-generation sequencing methods to leverage samples of a taxon at their center of maximum diversity to explore phylogenetic relationships and a possible mechanism of coexistence. LOCATION Flint Island, Southern Line Islands, Republic of Kiribati. METHODS A comprehensive review of museum records, the primary literature, and unpublished field survey records was undertaken to determine ranges for four "arc-eye" hawkfish species in the Paracirrhites species complex and a potential hybrid. Fish from four Paracirrhites species were collected from Flint Island in the Southern Line Islands, Republic of Kiribati. Hindgut contents were sequenced, and subsequent metagenomic analyses were used to assess the phylogenetic relatedness of the host fish, the microbiome community structure, and prey remains for each species. RESULTS Phylogenetic analyses conducted with recovered mitochondrial genomes revealed clustering of P. bicolor with P. arcatus and P. xanthus with P. nisus, which were unexpected on the basis of previous morphological work in this species complex. Differences in taxonomic composition of gut microbial communities and presumed prey remains indicate likely separation of foraging niches. MAIN CONCLUSIONS Our findings point toward previously unidentified relationships in this cryptic species complex at its proposed center of distribution. The three species endemic to the Polynesian province (P. nisus, P. xanthus, and P. bicolor) cluster separately from the more broadly distributed P. arcatus on the basis of relative abundance of metazoan sequences in the gut (presumed prey remains). Discordance between gut microbial communities and phylogeny of the host fish further reinforce the hypothesis of niche separation.
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Affiliation(s)
- Beverly J. French
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Yan Wei Lim
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Brian J. Zgliczynski
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
| | - Robert A. Edwards
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
- Department of Computer ScienceSan Diego State UniversitySan DiegoCAUSA
| | - Forest Rohwer
- Department of BiologySan Diego State UniversitySan DiegoCAUSA
| | - Stuart A. Sandin
- Center for Marine Biodiversity and ConservationScripps Institution of OceanographyUniversity of CaliforniaSan DiegoCAUSA
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Bourgarel M, Noël V, Pfukenyi D, Michaux J, André A, Becquart P, Cerqueira F, Barrachina C, Boué V, Talignani L, Matope G, Missé D, Morand S, Liégeois F. Next-Generation Sequencing on Insectivorous Bat Guano: An Accurate Tool to Identify Arthropod Viruses of Potential Agricultural Concern. Viruses 2019; 11:v11121102. [PMID: 31795197 PMCID: PMC6950063 DOI: 10.3390/v11121102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/12/2019] [Accepted: 11/26/2019] [Indexed: 12/13/2022] Open
Abstract
Viruses belonging to the Dicistroviridae family have attracted a great deal of attention from scientists owing to their negative impact on agricultural economics, as well as their recent identification as potential aetiological agents of febrile illness in human patients. On the other hand, some Dicistroviruses are also studied for their potential biopesticide properties. To date, Dicistrovirus characterized in African mainland remain scarce. By using High-Throughput Sequencing technology on insectivorous bat faeces (Hipposideros Caffer) sampled in a cave used by humans to collect bat guano (bat manure) as fertilizer in Zimbabwe, we characterized the full-length sequences of three Dicistrovirus belonging to the Cripavirus and Aparavirus genus: Big Sioux River Virus-Like (BSRV-Like), Acute Bee Paralysis Virus (ABPV), and Aphid Lethal Paralysis Virus (ALPV). Phylogenetic analyses of ORF-1 and ORF-2 genes showed a complex evolutionary history between BSRV and close viruses, as well as for the Aparavirus genus. Herewith, we provide the first evidence of the presence of Dicistrovirus in Zimbabwe and highlight the need to further document the impact of such viruses on crops, as well as in beekeeping activities in Zimbabwe which represent a crucial source of income for Zimbabwean people.
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Affiliation(s)
- Mathieu Bourgarel
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Centre International de Recherche Agronomique pour le Développement (CIRAD), Research Platform-Production and Conservation in Partership, Unité Mixe de Recherche ASTRE, Harare, Zimbabwe
| | - Valérie Noël
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Davies Pfukenyi
- Faculty of Veterinary Science, University of Zimbabwe, P.O. Box MP167, Mt. Pleasant Harare P.O. Box MP167, Zimbabwe; (D.P.); (G.M.)
| | - Johan Michaux
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; (J.M.); (A.A.)
| | - Adrien André
- Université de Liège, Laboratoire de Génétique de la Conservation, GeCoLAB, 4000 Liège, Belgium; (J.M.); (A.A.)
| | - Pierre Becquart
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Frédérique Cerqueira
- Institut des Sciences de l’Evolution de Montpellier (ISEM), Univ Montpellier, Centre National de Recherche Scientifique (CNRS), Ecole Pratique des Hautes Etude (EPHE)s, Institut de Recherche pour le Développement (IRD), 34398 Montpellier, France;
| | - Célia Barrachina
- Montpellier GenomiX (MGX), Biocampus Montpellier, Centre National de Recherche Scientifique (CNRS), Intitut National de la Santé et de la Recherche Médicale (INSERM), Univ Montpellier, 34094 Montpellier, France;
| | - Vanina Boué
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Loïc Talignani
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Gift Matope
- Faculty of Veterinary Science, University of Zimbabwe, P.O. Box MP167, Mt. Pleasant Harare P.O. Box MP167, Zimbabwe; (D.P.); (G.M.)
| | - Dorothée Missé
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
| | - Serge Morand
- Animal Santé Territoire Risque Environnement- Unité Mixe de Recherche 117 (ASTRE) Univ. Montpellier, Centre International de Recherche Agronomique pour le Développement (CIRAD), Institut National de la Recherche Agronomique, 34398 Montpellier, France; (M.B.); (S.M.)
- Institut des Sciences de l’Evolution de Montpellier (ISEM) Univ. Montpellier, Centre National de Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Centre International de Recherche Agronomique pour le Développement (CIRAD), 34000 Montpellier, France
| | - Florian Liégeois
- Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle- Unité Mixe de Recherche 224 (MIVEGEC), Institut de Recherche pour le Développement (IRD), Centre National de Recherche Scientifique (CNRS), Univ. Montpellier, 34398 Montpellier, France; (V.N.); (P.B.); (V.B.); (L.T.); (D.M.)
- Correspondence:
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