Guano morphology reveals ecological information in British bats

Ware, Roselyn; Garrod, Benjamin; Macdonald, Hannah; Allaby, Robin G.

doi:10.1101/728824

Cited by 2 publications

(3 citation statements)

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“…The need for identifying predators in insectivorous diet studies strongly depends on the sampling scheme and on the ecology of the targeted organisms. Such identification is especially important when using environmental samples, such as fecal samples, as it ensures that samples belong to the species of interest and it eliminates erroneous assignation of prey (Ware et al, 2019). For example, the metabarcoding study performed by Forin‐Wiart et al (2018) on cat fecal samples revealed that 2.4% of these belonged to another predator species despite a preselection of samples using qPCR screening.…”

Section: Discussionmentioning

confidence: 99%

“…While working with guano collected from roost sites, a potential problem arises from the fact that several bat species may roost in the same sites. Because guano is not easily distinguishable between bat species (Ware, Garrod, Macdonald, & Allaby, 2019), it is critical to identify bat species to avoid misassigning prey to the wrong bat species and also to discard guano samples that could be contaminated with excreta from other bat species. To this end, Galan et al.…”

Section: Introductionmentioning

confidence: 99%

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In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

Tournayre

Leuchtmann

Filippi‐Codaccioni

et al. 2020

Ecology and Evolution

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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.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

Tournayre

Leuchtmann

Filippi‐Codaccioni

et al. 2020

Ecology and Evolution

View full text Add to dashboard Cite

show abstract

“…The requirement for the molecular identification of predators in insectivorous diet analyses depends on the sampling scheme and on the ecology of these organisms. It is especially important when using environmental samples, such as faecal samples, to ensure that samples correspond to the species of interest and to avoid erroneous assignation of prey (Ware et al, 2019). For example, a metabarcoding study by Forin-Wiart et al (2018) on cat faecal samples revealed that 2.4% of these later belonged to another predator species.…”

Section: Discussionmentioning

confidence: 99%

In silicoand empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

Tournayre

Leuchtmann

Filippi‐Codaccioni

et al. 2019

Preprint

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This last decade, environmental DNA metabarcoding approaches have been developed and improved to minimize biological and technical biases; some challenges, however, remain, as the design of primers. Here we have performed a comprehensive assessment of ten COI and two 16S primer sets. We have combined in silico, in vivo-mock community of 33 arthropod taxa from 16 orders and guano analyses to identify primer sets that should maximize arthropod detection and taxonomic identification, whilst identifying bat species and minimizing labour time and cost. We have focused on two insectivorous bat species living in mixed-colonies, the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy’s bat (Myotis emarginatus). We have found that the level of primer degeneracy is the main factor influencing arthropod detection for in silico and mock community analyses, while the amplicon length is critical for the detection of arthropods from degraded DNA samples. Our results confirm the importance of performing predator detection and taxonomic identification, simultaneously with arthropod sequencing, as faeces samples can be contaminated by different insectivorous species. Moreover, amplifying bat DNA does not affect the primers’ capacity to detect arthropods. We therefore recommend the systematic simultaneous identification of predator and prey. Finally, we evidenced that one third of the prey occurrences are unreliable and probably not of primary interest in diet studies, which might decrease the relevance of combining several primer sets instead of using one efficient primer set. In conclusion, this study provides general criteria enabling the selection of primers whilst considering different scientific and methodological constraints.

show abstract

Guano morphology reveals ecological information in British bats

Cited by 2 publications

References 28 publications

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

In silicoand empirical evaluation of twelve COI & 16S metabarcoding primer sets for insectivorous diet analyses

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