Primer biases in the molecular assessment of diet in multiple insectivorous mammals

Browett, Samuel S. and Curran, Thomas G. and O’Meara, Denise B. and Harrington, Andrew P. and Sales, Naiara Guimarães and Antwis, Rachael E. and O’Neill, David and McDevitt, Allan D. (2021) Primer biases in the molecular assessment of diet in multiple insectivorous mammals. Mammalian Biology, 101 (3). pp. 293-304. ISSN 1616-5047

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Abstract

Our 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.

Item Type:	Article
Additional Information:	Funding Information: SSB was supported by a Pathway to Excellence PhD Scholarship from the University of Salford and TGC was supported by a Waterford Institute of Technology and Environmental Protection Agency (EPA) cofund PhD Scholarship, funded under the EPA Research Programme 2014–2020. The EPA Research Programme is a Government of Ireland initiative funded by the Department of the Environment, Climate and Communications. It is administered by the EPA, which has the statutory function of co-ordinating and promoting environmental research. Thanks to the local National Park and Wildlife Service (NPWS) conservation rangers for sampling bat droppings. Fieldwork in relation to shrew sampling was supported by grants from the Vincent Wildlife Trust and a Genetics Society Heredity Fieldwork Grant awarded to SSB and ADM. Laboratory work was supported by grants from Bat Conservation Ireland and a University of Salford Internal Research Award awarded to DBO’M and ADM, and a University of Salford Pump Priming award to ADM. NGS also thanks FCT/MCTES for the financial support to CESAM (UID/AMB/50017/2019), through national funds. Finally, we are grateful to the reviewers for their valuable and constructive comments which improved the manuscript. Funding Information: SSB was supported by a Pathway to Excellence PhD Scholarship from the University of Salford and TGC was supported by a Waterford Institute of Technology and Environmental Protection Agency (EPA) cofund PhD Scholarship, funded under the EPA Research Programme 2014?2020. The EPA Research Programme is a Government of Ireland initiative funded by the Department of the Environment, Climate and Communications. It is administered by the EPA, which has the statutory function of co-ordinating and promoting environmental research. Thanks to the local National Park and Wildlife Service (NPWS) conservation rangers for sampling bat droppings. Fieldwork in relation to shrew sampling was supported by grants from the Vincent Wildlife Trust and a Genetics Society Heredity Fieldwork Grant awarded to SSB and ADM. Laboratory work was supported by grants from Bat Conservation Ireland and a University of Salford Internal Research Award awarded to DBO?M and ADM, and a University of Salford Pump Priming award to ADM. NGS also thanks FCT/MCTES for the financial support to CESAM (UID/AMB/50017/2019), through national funds. Finally, we are grateful to the reviewers for their valuable and constructive comments which improved the manuscript. Publisher Copyright: © 2021, The Author(s).
Uncontrolled Keywords:	/dk/atira/pure/subjectarea/asjc/1100/1105
Departments or Groups:
Depositing User:	Admin SSL
Date Deposited:	19 Oct 2022 23:13
Last Modified:	10 Aug 2023 22:25
URI:	http://repository-testing.wit.ie/id/eprint/4716

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