DOI: 10.5061/dryad.pvmcvdnmr
title: Data for Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach

description: 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 increasing distance between sites. The
 distance decay of similarity derived from eDNA was similar and even more
 pronounced than that obtained with capture-based methods (gill-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 provides
 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.
description: The detailed methods explainning how this dataset was collected
 can be found in the methods section of
 <strong>Cantera</strong>, I., Decotte, J., Dejean, T.,
 Murienne, J., Vigouroux, R., Valentini, A., Brosse, S. (2022).
 Characterizing the spatial signal of environmental DNA in river systems
 using a community ecology approach. <strong><em>Molecular
 Ecology Resources</em></strong> 22, 1274–1283.
description: # Data for Characterizing the spatial signal of environmental DNA in river
 systems using a community ecology approach ## Description of the data and
 file structure The dataset contains the following files: ### **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