Results
Carrion fly 12S metabarcoding resulted in 16,130,638 paired sequence
reads from 368 pooled samples. The average read depth per sample
replicate was 21,976 reads. The sandfly 12S metabarcoding results showed
25,093,673 paired sequence reads from 943 pooled samples and the average
read depth per sample replicate is 13,780 reads. Finally, mosquito 12S
metabarcoding results resulted in 35,132,064 total paired sequence reads
from 322 pooled samples with an average read depth per sample replicate
of 55,152 reads.
After conservative quality measures designed to clean the raw data, the
following datasets were used for analysis (and excluded human DNA):
carrion fly data had 5,010,458 total paired sequences from 265 pooled
samples which represented 37 of the 39 sites; the sandfly data had
5,233,020 total paired sequences from 354 pooled samples which
represented 36 sites; finally, the mosquito data had 6,254,399 paired
sequences from 78 pooled samples which represented 25 sites (a summary
of site-level data for each iDNA method can be found in Appendix S1:
Table S1). Pooled samples of carrion flies showed the highest
amplification success followed by pooled sandfly samples and finally
pooled mosquito samples (Table 1), although these results exclude human
DNA which made up the majority of sequence reads in the mosquito
dataset.