DOI: 10.5061/dryad.zkh1893g2
title: Populations genomics of deep-sea hydrothermal vent copepod Stygiopontius lauensis: from raw fasta files to filtered vcf file

description: Copepoda is the most abundant taxon in deep-sea hydrothermal vents, where
 hard substrate is available. Despite the increasing interest in seafloor
 massive sulphides exploitation, there have been no population genomic
 studies conducted on vent meiofauna, which are known to contribute over
 50% to metazoan biodiversity at vents. To bridge this knowledge gap,
 restriction site-associated DNA sequencing, specifically 2b-RADseq, was
 used to retrieve thousands of genome-wide single nucleotide polymorphisms
 (SNPs) from abundant populations of the vent-obligate copepod
 Stygiopontius lauensis from the Lau Basin. SNPs were used to investigate
 population structure, demographic histories, genotype-environment
 associations at a basin scale. Genetic analyses also helped to evaluate
 the suitability of tailored larval dispersal models and the
 parameterization of life history traits that better fit the population
 patterns observed in the genomic dataset for the target organism. Highly
 structured populations were observed on both spatial and temporal scales,
 with divergence of populations between the north, mid, and south of the
 basin estimated to have occurred after the creation of the major transform
 fault dividing the Australian and the Niuafo’ou tectonic plate (350 kya),
 with relatively recent secondary contact events (&lt; 20 kya). Larval
 dispersal models were able to predict the high levels of structure and the
 highly asymmetric northward low-level gene flow observed in the genomic
 data. These results differ from most studies conducted on megafauna in the
 region, elucidating the need to incorporate smaller size when considering
 site-prospecting for deep-sea exploitation of seafloor massive sulphides,
 and the creation of area-based management tools to protect areas at risk
 of local extinction, should mining occur.
description: This dataset was collected by implementing a modified (for the
 target species) version of the original 2b-RAD protocols (Wang et al.,
 2012) on 149 individuals of Stygiopontius lauensis copepods. These were
 collected from hydrothermal vents in the Lau Basin (Southwest Pacific
 Ocean). The pooled library was composed of samples collected in 2016 and
 in 2019. Samples from 2016 were sequenced on an Illumina Nextseq 500,
 while those from 2019 were sequenced on an Illumina Nextseq 2000 at
 University Medical Centre, Utrecht (UMC). Samples were demultiplexed by
 UMC. Raw fastq files were further demultiplexed by specimen using a
 modified script that implements <em>Cutadapt, </em>finding
 specimen-specific barcodes. These files were then filtered for low-quality
 reads and duplicates in the same script, resulting in 149 fasta files
 being used for downstream analysis.  Fasta files were
 run through DiscoSnpRad++ using a kmer length of 15, and an auto read
 depth. The resulting vcf file was then run through the DiscoSnpRad
 postprocessing scripts to generate a vcf file containing 1 SNP per locus.
 This resulting vcf file was filtered for missing data (cutoff = 0.3) and
 heterozygosity (cutoff = 0.6). Individuals with data &gt; 0.5 were
 also removed. 
description: # Populations genomics of deep-sea hydrothermal vent Copepod Stygiopontius
 lauensis: from raw fasta files to filtered vcf file
 [https://doi.org/10.5061/dryad.zkh1893g2](https://doi.org/10.5061/dryad.zkh1893g2) ## Description of the data and file structure This dataset contains Fasta files which are demultiplexed by specimen and labeled as follows: specimen_ventsite_filtered/notfiltered. Where the samples are filtered, they are filtered by GC content (RADs with GC higher than 50% were removed). These files are the raw files used for all analyses in the study. Additionally, a popmap.txt file can be found containing the mapping information needed to group the Fasta files and subsequent genotypes by metadata of the vent site and year collected. For population genomics, either a global alignment method such as STACKS2 or a k-mer-based approach for calling Single Nucleotide Polymorphisms (SNPs) such as DiscoSnpRAD++ can be applied to the raw fasta files following the instructions for each software that can easily be found on the following webpages (the output will be a Variant Calling File (VCF) or any other file type of your choose depending on the type of downstream analysis: STACKS2: [https://catchenlab.life.illinois.edu/stacks/](https://catchenlab.life.illinois.edu/stacks/) DiscoSnpRAD++: [https://github.com/GATB/DiscoSnp](https://github.com/GATB/DiscoSnp) To apply simple population genomics analysis pertaining to population structure, the vcf file can be read into SNPrelate in R. To apply demographic analyses, the following scripts can be applied directly to the vcf file: [https://github.com/Atranluy/Scripts-Ifremeria](https://github.com/Atranluy/Scripts-Ifremeria) ## Sharing/Access information n/a ## Code/Software n/a