DOI: 10.5061/dryad.j0zpc86q1
title: Mosquito iDNA reveals landscape patterns of birds and mammals

description: Changes in fire regimes and the introduction of invasive species are
 negatively impacting Northern Australia's biota, highlighting the
 need for reliable biodiversity monitoring data. Here we used
 mosquito‐ingested DNA (iDNA) to detect birds and mammals within Kakadu
 National Park. Six sites were sampled on two occasions (wet and dry
 season), with three traps deployed for two consecutive nights of sampling
 at each site. Mosquitoes were processed in bulk samples per trap ranging
 from 31 to 1987 mosquitoes. Extracted DNA was amplified using primers
 targeting vertebrates (12SV5), mammals (16SMam1/2) and birds (Aves01) with
 iDNA‐derived richness and composition measured. A total of 50 avian and 19
 mammalian taxa were detected, including threatened species such as the
 white‐throated grasswren (Amytornis woodwardi) and the ghost bat
 (Macroderma gigas), along with difficult‐to‐monitor groups such as
 small‐bodied and arboreal mammals. Community composition was shown to be
 distinct between sampling events, and avian richness was higher during the
 dry season. Importantly for the management of the park, our findings
 suggest that fire regimes modified both bird and mammal communities during
 the dry season, with vegetation structure being correlated with avian and
 mammalian community composition during the wet season. This study
 highlights the capacity for iDNA metabarcoding to provide fine‐scale
 ecologically relevant information within a large, dynamic and
 difficult‐to‐access landscape
description: Bulk mosquito samples were collected from six 1ha sites across
 two field campaigns undertaken during a wet and dry season. At each site
 three EVS traps were set up and samples were collected for two consecutive
 nights. A total of 71 bulk samples were collected and processed using a
 salting out procedure that could be adapted for the variability in the
 size of the bulk samples. Samples were PCR'd using three primers
 (12SV5, 16SMam1/2 and Aves01), with all PCRs performed in triplicates. PCR
 product was cleaned using a Minielute kit and the three primers were
 pooled equamolar. Before being sent to the Ramaciotti centre for genomics
 where they were sequenced on a Novaseq 6000 sequencing run. Raw sequencing
 data was firstly processed using OBITools, with the steps briefly
 including reassembling paired ended reads, removal of poor quality reads,
 assignment of reads to their relvant primer and sample, dereplication of
 reads and initial taxonomic assignments. Following processing through
 OBITools samples were clustered into MOTUs using SUMACLUST applying a 97%
 similarity threshold. Data was then further cleaned using MetabaR. The
 three primers were then merged to form an avian and mammalian
 dataset.
description: # Mosquito iDNA reveals landscape patterns of birds and mammals
 [https://doi.org/10.5061/dryad.j0zpc86q1](https://doi.org/10.5061/dryad.j0zpc86q1) ## Description of the data and file structure Data presents birds and mammals detected from iDNA from bulk mosquito samples collected from six sites across two sampling periods, representative of the wet and dry seasons in Kakadu National Park. ### Files and variables #### File: RM-environmentaldata-nightsmerged-correct.csv **Description:** vegetation characteristics and recent fire regimes of the six sites sampled in Kakadu National Park ##### Variables * Sample: name of sample * Site: which site it was collected from S1, S3, S4, S5, S7, S8 * Season: if the data corresponds to the wet or dry season  * Night * Fire: degree of burning observed during the dry season * Stem.density: the number of trees wider than 10cm in width * Total.overstorey: the percentage of overstorey cover * Understoreycover: the percentage of understorey cover * Veg.richness: the total number of different plant species * Ground.cover.richness: the number of different ground cover plant species * Mid.storey.richness: the number of different mid-storey plant species * Canopy.richness: the number of different canopy plant species #### File: RM_mozzies_S1_L001_R1_001.fastq.gz **Description:** sequencing lane 1 of the Novaseq6000 run with the reads 1 of the paired-end reads #### File: RM_mozzies_S1_L001_R2_001.fastq.gz **Description:** sequencing lane 1 of the Novaseq6000 run with the reads 2 of the paired-end reads #### File: RM_mozzies_S1_L002_R1_001.fastq.gz **Description:** sequencing lane 2 of the Novaseq6000 run with the reads 1 of the paired-end reads #### File: RM_mozzies_S1_L002_R2_001.fastq.gz **Description:** sequencing lane 2 of the Novaseq6000 run with the reads 2 of the paired-end reads #### File: RM_12SV5_ngsfilter.txt **Description:** mapping file for the 12SV5 primers targeting vertebrate DNA to be used with the *ngsfilter* command in OBITools #### File: RM_16SMam_ngsfilter.txt **Description:** mapping file for the 16SMam1/2 primers targeting mammal DNA to be used with the* ngsfilter* command in OBITools #### File: RM_Aves01_ngsfilter.txt **Description:** mapping file for the Aves01 primers targeting bird DNA to be use with the* ngsfilter* command in OBITools #### File: RM-allbirds-reads-nightsmerged.csv **Description:** table of merged avian taxa from the 12SV5 and Aves01 primers, columns dictate taxa, rows dictate mosquito traps with the two nights of sampling merged, numbers indicate read count from the merged datasets #### File: RM-allmammals-reads-nightsmerged.csv **Description:** table of merged mammalian taxa from the 12SV5 and 16SMam1/2 primers, columns dictate taxa, rows dictate mosquito traps with the two nights of sampling merged, numbers indicate read count from the merged datasets ## Software Raw sequencing data presented in the fastq.gz files can be imported into OBITools 3 and processed accordingly, with sequences demultiplexed and assigned to the relevant primer/sample using the* ngsfilter* command utilising the ngsfiles provided. All data used for analysis is provided in the form of a .csv file and can be opened with relevant software, including Excel and R.