Table 1.
A list of attributes of all samples based on Illumina MiSeq sequencing and metabarcoding analysis.
Only the 41 samples for which library amplification was successful are listed. System = Major river system, given for the Zamora samples; Reads = total reads assigned to the sample; % target = reads forming clusters of more than 10 reads that were successfully identified in the tree-based approach; H' = Shannon diversity index.
Fig 1.
Box plots of some characteristics of old vs. new samples: Total reads per sample, percent of target reads, OTUs, and Shannon diversity index.
Values marked with an asterisk (*) have a significantly higher median in fresh samples (P ≤ 0.05). Top row: all samples; bottom row: only samples from Zamora.
Fig 2.
Distribution of divergence (branch lengths) of terminal branches in all sequences of the reference tree and in query sequences.
The threshold branch length marking the 99.9% quantile of all reference sequences, shown in both plots with a vertical red line, is 0.773. Query sequences with branch lengths above the threshold are considered misidentified.
Table 2.
Taxonomic composition of the samples, grouped by insect orders and the non-insect groups Annelida, and Crustacea (paraphyletic).
Values given are absolute number of species of a group detected in a sample, with proportional number of reads representing this group in brackets.
Table 3.
The OTUs registered with most sequencing reads and detected in most samples.
Fig 3.
A subset of the reference tree for visualization of the identification of query sequences.
Reference sequences in black, query sequences with number of sample, number of ID, number of sequence, and number of assembled reads in blue. A: In many cases, query sequences cluster with the closest reference sequence with branch lengths shorter than interspecific divergences. B: Query sequences with very long branches separating them from reference sequence are discarded as likely misidentifications.