DOI: 10.5061/dryad.7d7wm37ts
title: Primer biases in the molecular assessment of diet in multiple insectivorous mammals

description: 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 suggest 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.
description: This is a metabarcoding dataset for Browett SS, Curran TG, O’Meara
 DB, Harrington AP, Sales NG, Antwis
 RE, O’Neill D, McDevitt AD (2021) Primer biases in the molecular
 assessment of diet in multiple insectivorous mammals.
 <i>BioRxiv</i><i>, </i>Doi:
 10.1101/2021.01.18.426998 DNA was
 extracted from faeces of 24 bats (<i>Rhinolophus
 hipposideros</i>) and gut contents of 27 shrews (<em>Sorex
 minutus</em> and <em>Crocidura russula</em>). The COI
 region was amplified using 2 primer sets, referred to as Gillet and Zeale.
 There are four multiplexed fastq files. A forward and reverse for the 24
 bats and a forward and reverse for the 27 shrews. Samples were multiplexed
 using primers with dual-index 8 base pair MID tags on them. The sequences
 contain the primer region and MID tags. A file with the list of tags and
 primer sequence is included. Sequencing adapters were ligated using a
 PCR-free method. Library was sequenced on an Illumina MiSeq V2 300 cycle
 kit. For full details on data collection, preparation
 and sequencing, see https://doi.org/10.1101/2021.01.18.426998 (and
 forwarding link to published article)
 and https://github.com/ShrewlockHolmes/ Further
 information on samples is also available
 from https://github.com/ShrewlockHolmes/
description: The list containing the MID tags and individual sample names are
 included. The columns are 1: Primer used
 2: Sample ID 3: Forward MID tag
 4: Reverse MID tag 5: Forward primer
 sequence 6: Reverse primer sequence
 7:9 misc info required for pipeline used for article.