Fine-scale environmentally associated spatial structure of Lumpfish ( Cyclopterus lumpus) across the Northwest Atlantic

Lumpfish, Cyclopterus lumpus, have historically been harvested throughout Atlantic Canada and are increasingly in demand as a solution to controlling sea lice in Atlantic salmon farms – a process which involves both the domestication and the transfer of lumpfish between geographic regions. Here, we have 70K SNP array data and whole genome re-sequencing data (WGS) for a variety of sample sites across the Northwest Atlantic. 

Methods
We sampled 1115 individuals from 79 locations throughout the North Atlantic from 2009 to 2019 (Fig. 1a; S1) in conjunction with scientific research surveys (trawl and beach seines) and commercial fishing activities. Sampling locations included waters around Newfoundland (N=994), the Gulf of St. Lawrence (GSL) (N=108), waters around Grand Manan (N=13), and from the Gulf of Maine (N=83). Due to the different sampling approaches utilized, differences in the sexes and life stages collected were present. Research vessel surveys collected individuals using a bottom trawl and generally targeted adults of both sexes, commercial samples were largely adult females due to the selective nature of the fishery for roe, and coastal sites around Newfoundland (TNR, SPA, and NMS, Fig. 1a), sampled using a beach seine were juvenile lumpfish comprising both sexes. In all cases, fin clips were preserved in 95% ethanol for subsequent DNA extraction.

            For the 70K SNP array data, DNA extractions were performed using DNeasy Blood and Tissue kits (Qiagen) according to manufacturer’s protocols. Genomic DNA was visualized by 1% agarose gel electrophoresis and quantified using Quant-iT PicoGreen ds-DNA Assay kits (Thermofisher) on a fluorescent plate reader. Genomic DNA was normalized to 15 ng/ml and sent to the Centre of Integrative Genomics (CIGENE, Ås, Norway) for genotyping on the lumpfish 70K SNP Affymetrix Axiom array (produced by CIGENE and Aquagen; Holborn et al., 2022). 

            We conducted medium coverage (~8x), whole genome re-sequencing (WGS) of 848 lumpfish from multiple sites across North America (Fig. 1a; S1). The same individuals were used for WGS as in the array; however, individuals from sites US1, US2, CA and BHbr, were only present with array data. For whole genome re-sequencing library preparation, DNA extraction followed Mayjonade et al. (2016), using Longmire’s buffer (Longmire et al., 1997) for tissue lysis. Library preparation followed a modification of the protocol from Therkildsen and Palumbi (2017) by scaling down Nextera DNA Flex Library Prep Kits (Illumina) reaction volumes to 0.13x then used a standard volume in the Illumina protocol. We then used Kapa Hi-Fidelity Library Amplification Kits (Roche) for library amplification (20 ml reactions, 4 ml Nextera Unique Dual Indexes Set A (Illumina)). Libraries were quantified by Qubit (ThermoFisher) and an Agilent Bioanalyzer was used to check average fragment size. Libraries were normalized from 96-well plates to equimolar concentrations and pooled separately for each lane of sequencing. We sequenced pooled libraries at The Genome Quebec Centre d’expertise et de services on 11 lanes of an Illumina NovaSeq6000 S4.