DOI: 10.5061/dryad.x3ffbg7rr
title: Data from: Mosquito derived ingested DNA as a tool for monitoring terrestrial vertebrates within a peri-urban environment

description: Global biodiversity is declining at an alarming rate. Consequently, there
 is a pivotal need to determine the occurrences and distributions of
 threatened species. Monitoring and detection approaches are traditionally
 reliant on capture (traps and cameras), as well as observations. However,
 these approaches are time consuming and skewed towards the detection of
 large and/or common species. Invertebrate ingested DNA (iDNA) is being
 increasingly used as a novel approach for indirectly monitoring
 terrestrial vertebrates via their DNA in invertebrates with hematophagous,
 coprophagous or saprophagous feeding strategies. This study aimed to
 examine the vertebrate diversity which could be retrieved using mosquito
 derived iDNA in a peri-urban setting. Furthermore, the study also examined
 the influence of a human blocking primer and the application of multiple
 primers on the detection of the targeted taxa. Sampling was performed in
 Sydney, Australia, in a peri-urban environment adjacent to both urbanised
 and protected environments. As a means of ensuring that sampling could be
 performed by non-scientists, domestically available light traps were used.
 In total, 118 mosquitoes were captured. DNA was extracted from individual
 mosquitoes and amplified using four different primers, targeting
 vertebrates, mammals and birds, with and without a human blocking primer
 (except for the bird PCRs).The overall diversity retrieved reveals a broad
 diversity of species with ten avian taxa and six mammalian taxa, including
 both native and non-native species of varying body sizes and behavioural
 characteristics. Both the multi-locus approach and the use of a human
 blocking primer revealed additional diversity. The use of iDNA offers the
 potential as an important tool for local land managers and citizen science
 projects for the monitoring of vertebrates. 
description: # Mosquito derived ingested DNA (iDNA) as a tool for monitoring
 terrestrial vertebrates within a peri-urban environment
 [https://doi.org/10.5061/dryad.x3ffbg7rr](https://doi.org/10.5061/dryad.x3ffbg7rr) **Description of the data and file structure** This data set comprises three different groups of data \- FASTQ files generated from the sequencing of each library \- Mapping files for each amplicon allowing sequenced reads to be demultiplexed and assigned to samples in OBITools \- Clean data sets for each amplicon after being processed through OBITools and MetabaR The FASTQ files originate from three libraries, the name of each library, corresponding files and the relevant amplicon sequenced in that library are as follows: **CHI9961A1** - this library was sequenced on the Nextseq platform - this folder includes sequences from four lanes of sequencing denotated by L001, L002 etc. each lane has a corresponding R1 and R2 file relating to the bi-directional raw reads. The following amplicons were sequenced as part of this library - 12SV5 (no blocking primer), 16SMam1/2 (no blocking primer) and 16SP007 (no blocking primer) **CHI9961A2** - this library was sequenced on the Nextseq platform - this folder includes four lanes of sequencing denoted by L001, L002 etc. each lane has a corresponding R1 and R2 file relating to the bi-directional raw reads. The following amplicons were sequenced as part of this library - 16S Mam1/2 (with blocking primer), 16SP007 (with blocking primer) **CHI11030A1** - this library was sequenced on the Miseq platform and includes just the relevant R1 and R2 files. This library includes the following amplicons - 12V5 (with blocking primer), Aves01 The **KWG_mapping_files.zip** is a zip folder containing the mapping files to use in OBITools, each amplicon has a corresponding mapping file provided in a .txt format, it can be identified by the name of amplicon and NGS file at the end. For the three amplicons sequenced both with and without a human blocking primer the same mapping file can be used for each except for 16SP007 which has separate mapping files for the unblocked and blocked dataset. The **KWG-clean_data_outputs.zip** is folder containing the clean datasets for each amplicon. Each clean dataset is provided in a .csv file denoted by the name of the amplicon, the file name will also denote if the dataset relates to the amplicon with/without a human blocking primer.