22 July 2020 README file written by Joanne Littlefair, Queen Mary University of London Email j.e.littlefair@qmul.ac.uk for questions and collaborations! This dryad file refers to data published in Molecular Ecology manuscript ID MEC-20-0459 Thermal stratification and fish thermal preference explain vertical eDNA distributions in lakes Joanne Littlefair, Lee Hrenchuk, Paul Blanchfield, Michael Rennie, Melania Cristescu We have uploaded raw zipped fastq files from our project which contain the results of our sequencing. Each file has a unique name which corresponds to sequencing name, indexing combination, year and season of collection, lake, depth position and sample number. For example: MI.M00833_0814.001.N704---S502.D18AUG23914_R2.fastq.gz * MI.M00833_0814.001 - this refers to the sequencing lane. There are five lanes in this project. * N704---S502 - this refers to the combination of dual Nextera (Illumina) forward and reverse indices used. * D18AUG - this refers to the year (18 for 2018, 17 for 2017) and season (AUG for summer stratification, OCT for autumn turnover) of sample collection. * 239 - the next three digits refer to the lake the sample was collected in at the IISD Experimental Lakes Area. Possible values are 223, 239, 224, 626 or 373. * 14 - the next two numbers refer to the sampling depth and sample number. The first number refers to the sampling depth. Possible values include 1, 2, 3, 4, 5, 6. These refer to relative vertical positions in the water column. Lakes were different depths, so the absolute depths will differ (see explanation in manuscript). 1 refers to the shallowest depth at the surface, 6 refers to the deepest depth. For a list of absolute depths of the samples from each lake, refer to Table S3 in the supplementary material. The second number refers to the biological replicate (water sample). Possible values are 1, 2, 3, 4. * The final two characters (R1 or R2) refer to forward and reverse sequencing files. * So for example, this file contains the sequences from the water sample collected in August 2018 from lake 239 at the shallowest depth (1) and the fourth biological replicate. There are 672 eDNA files labelled in this way (forward and reverse for 336 samples). Negative controls are also included. For each lake and season, all the field, extraction and PCR negative controls were sequenced in a single library. These are labelled slightly differently. For example: MI.M00833_0814.001.N702---S507.D18OCT239BLANK_R1.fastq.gz * This part of the file name (MI.M00833_0814.001.N702---S507.D18OCT239) is identical to the eDNA format described above. * The code BLANK indicates it is a negative control sample. * So for example, this file contains the negative controls from lake 239 collected in October 2018. There are also two replicates of a mock community. These contain the code STRATMC. There are two replicates (1 or 2). The expected composition of the mock community libraries is given in Table S4. Table of sample x ELA ASV counts.csv * This is an ASV x sample table of counts. This contains the numbers of sequences from each ASV found in each sample. Only ASVs which matched to the database of fish found at IISD-ELA were included. * Both blank and eDNA samples are included. * The sample codes are used in the same way as above. So for example: * D17AUG23911 * This sample refers to water collected in 2017 in August, from lake 239, at depth 1 (the shallowest depth) and biological replicate 1. * There is also information on the taxonomic assignments given to each ASV. Table of sample x ALL ASV counts.csv * This is a similar ASV x sample table of counts. However, all ASVs are included, not just those which matched to fish found at IISD-ELA. * Therefore non-target taxa are present in this table. all_lengthfilter_zotus_4.fasta * This is a list of the sequence compositions of each ZOTU. It contains all the ASVs, not just those which matched to fish found at IISD-ELA.