DOI: 10.5061/dryad.nk98sf7vr
title: Raw sequencing data for assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies

description: Technological advances are enabling ecologists to conduct large-scale and
 structured community surveys. However, it is unclear how best to extract
 information from these novel community data. We metabarcoded 48 vertebrate
 species from their eDNA in 320 ponds across England and applied the
 'internal structure' approach, which uses joint species
 distribution models (JSDMs) to explain compositions as the result of four
 metacommunity processes: environmental filtering, dispersal, species
 interactions and stochasticity. We confirm that environmental filtering
 plays an important role in community assembly, and find that species'
 estimated environmental preferences are consistent with known ecologies.
 We also detect negative biotic covariances between fish and amphibians
 after controlling for divergent environmental preferences, consistent with
 predator-prey interactions (likely mediated by predator avoidance
 behaviour), and we detect high spatial autocorrelation for the palmate
 newt, consistent with its hypothesised relict distribution. Promisingly,
 ecologically and spatially distinctive sites are better explained by their
 environmental covariates and geographic locations, respectively, revealing
 sites where environmental filtering and dispersal limitation act more
 strongly. These results are consistent with the recent proposal that
 applying JSDMs to species distribution patterns can help reveal the
 relative importance of environmental filtering, dispersal limitation and
 biotic interaction processes for individual sites and species. Our results
 also highlight the value of the modern interpretation of metacommunity
 ecology, which embraces the fact that assembly processes differ among
 species and sites. We discuss how novel community data allow for several
 study design improvements that will strengthen the inference of
 metacommunity assembly processes from observational data.
description: # Raw sequencing data for assembly processes inferred from eDNA surveys of
 a pond metacommunity are consistent with known species ecologies The
 datasets contain all the raw sequencing data used for the study
 'Assembly processes inferred from eDNA surveys of a pond
 metacommunity are consistent with known species ecologies'. PCR
 amplification was performed using a two-step protocol targeting a 73-110
 bp fragment of 12S ribosomal RNA for vertebrates (Riaz et al. 2011). The
 data can be run through a standard metabarcoding pipeline such as Begum
 and OBITools, codes for execution and analysis can be found at
 [https://doi.org/10.5281/zenodo.7728859](https://doi.org/10.5281/zenodo.7728859). Data sets included: 5 sub-sets of raw pair-end sequencing data sequenced on the Illumina HiSeq platform using PE150. "UKpondsmetabarcodingmctrawdata.zip" includes five .zip files (p1.zip, p2.zip, p3.zip, p4.zip, p5.zip), each a sub-dataset containing approximately 96 eDNA samples. Five sub-datasets are in the same format, R1.fq.gz and R2.fq.gz are the pair-end files sequenced on the Illumina HiSeq platform using PE150. **Here is the structure of sub-dataset p1:** ./p1.zip #raw sequencing data for sample 1-96. 1p1_FDDP190656076-1a_1.clean.fq.gz #One pair-end file for p1 sub-dataset for library replication one. 1p1_FDDP190656076-1a_2.clean.fq.gz #Another pair-end files for p1 sub-dataset for library replication one. 1p2_FDDP190656077-1a_1.clean.fq.gz #One pair-end file for p1 sub-dataset for library replication two. 1p2_FDDP190656077-1a_2.clean.fq.gz #Another pair-end files for p1 sub-dataset for library replication two. 1p3_FDDP190656078-1a_1.clean.fq.gz #One pair-end file for p1 sub-dataset for library replication three. 1p3_FDDP190656078-1a_2.clean.fq.gz #Another pair-end files for p1 sub-dataset for library replication three. **p2.zip to p5.zip have the same structure as p1.zip, but for different samples.** ./p2.zip #raw sequencing data for sample 97-193. ./p3.zip #raw sequencing data for sample 194-288. ./p4.zip #raw sequencing data for sample 289-385. ./p5.zip #raw sequencing data for sample 386-481.