Shi, Y., Hoareau, Y., Reese, E.M. et al. Prey partitioning between sympatric wild carnivores revealed by DNA metabarcoding: a case study on wolf (Canis lupus) and coyote (Canis latrans) in northeastern Washington. Conserv Genet (2021). https://doi.org/10.1007/s10592-021-01337-2
./nc_raw/: this directory contains raw sequence data from PCR products of negative controls (N=100), including extraction and PCR negative controls;
canid.diet.obitools.tab: read count table of 374 MOTUs after obitools filtering;
MOTUS_N374.fasta: fasta file of 374 MOTUs;
taxonomy_MOTUs_N348.csv: taxonomy classification of 348 MOTUs. Note: 26 out of 374 MOTUs were removed because they could not be assigned to any taxon with at least 98% identity.
meta_N202.csv: meta information of 202 samples;
canid.diet.postFiltering.tab : final MOTU read count table, consisting of 332 MOTUs and 1037 PCR replicates across 202 samples.
canid.diet.postFiltering_long.csv: final MOTU read count table in the long format along with meta information;
canid.diet.presence.long.csv: final presence/absence data;
byspecies.freq.csv: frequency of occurrence data of 19 prey items in wolf and coyote;
1_obitools.sh: sequence data processing using the OBITools package;
2_filtering.r: data filtering to control for potential contamination and generate the final MOTU read count table;
3_blocking.r: assess the effects of predator-specific blocking primer and convert read count data to presence/absence data. Output: Fig.2 and Supplementary Table 1;
4_dietByspecies.r: assess the interspecific dietary differences between wolves and coyotes. Output: Fig.3;
5_diet_sig.r: PERMANOVA and SIMPER tests. Output: Fig.4, Supplementary Table 2 and Supplementary Table 3;
6_rra.r: Comparison of dietary profiles using FOO vs. RRA. Output: Supplementary Fig. 1