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Data for Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

Citation

Cantera, Isabel (2021), Data for Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach , Dryad, Dataset, https://doi.org/10.5061/dryad.pvmcvdnmr

Abstract

Environmental DNA (eDNA) is gaining a growing popularity among scientists but its applicability to biodiversity research and management remains limited in river systems by the lack of knowledge about the spatial extent of the downstream transport of eDNA.

Here, we assessed the ability of eDNA inventories to retrieve spatial patterns of fish assemblages along two large and species rich Neotropical rivers. We first examined overall community variation with distance through the distance decay of similarity and compared this pattern to capture-based samples. We then considered previous knowledge on individual species distributions, and compared it to the eDNA inventories for a set of 53 species.

eDNA collected from 28 sites in the Maroni and 25 sites in the Oyapock rivers permitted to retrieve a decline of species similarity with distance between sites. The distance decay of similarity derived from eDNA was similar, and even more pronounced, than that obtained with capture-based methods (gil-nets). In addition, the species upstream-downstream distribution range derived from eDNA matched to the known distribution of most species.

Our results demonstrate that environmental DNA does not represent an integrative measure of biodiversity across the whole upstream river basin but provide a relevant picture of local fish assemblages. Importantly, the spatial signal gathered from eDNA was therefore comparable to that gathered with local capture based methods, which describes fish fauna over a few hundred metres.

Methods

Sequencing information for each sample

Table with 1)Sample_code, 2)PCR_replicate_number, 3)Site_name, 4)River, 5)Sampling date, 6)Tag, 7)Run_name, 8)Type.

The samples used in this study are the samples having a code in the “Sample_code” column. Samples having “CNEG” value correspond to negative control samples and Samples having “Other” do not concern this study.

 

Run AIMI-72

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AIMI-73

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AOHX-1

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AOHX-2

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AOHX-5

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AOHX-8

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run AOHX-9

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

Run HVO-151

Compressed file containing 4 files corresponding to 4 Lanes files. Each line file contains: 1) Forward sequence file; 2) Reverse sequence file.

Run HVO-152

Compressed file containing 4 files corresponding to 4 Lanes files. Each line file contains: 1) Forward sequence file; 2) Reverse sequence file.

Run HVO-153

Compressed file containing 4 files corresponding to 4 Lanes files. Each line file contains: 1) Forward sequence file; 2) Reverse sequence file.

Run JHV-1

Compressed file containing: 1) Forward sequence file; 2) Reverse sequence file.

 

Sequence reference database

File containing the sequence reference database for Guianese freshwater fish species. The database contains 1593 sequences corresponding to 264 species.

sequence_reference_database_French_Guiana.txt

 

Results of taxonomic assignments

For each river, a table with the number of reads detected for each taxon in each field replicate (2 eDNA replicates were sampled per site). The table also indicates the number of PCR replicates in which the taxon was detected for each sample. The tables were made after the MOTU assignment to our reference database.

File names:                 maroni_reads_replicates_lv.csv

oyapock_reads_replicates_lv.csv