Genomic insights on conservation priorities for North Sea houting and European lake whitefish (Coregonus spp.)

Population genomics analysis holds great potential for informing conservation of endangered populations. We focused on a controversial case of European whitefish (Coregonus spp.) populations. The endangered North Sea houting is the only coregonid fish that tolerates oceanic salinities and was previously considered a species (C. oxyrhinchus) distinct from European lake whitefish (C. lavaretus). However, no firm evidence for genetic-based salinity adaptation has been available. Also, studies based on microsatellite and mitogenome data suggested surprisingly recent divergence (ca. 2,500 years bp) between houting and lake whitefish. These data types furthermore have provided no evidence for possible inbreeding. Finally, a controversial taxonomic revision recently classified all whitefish in the region as C. maraena, calling conservation priorities of houting into question. We used whole genome and ddRAD sequencing to analyze six lake whitefish populations and the only extant indigenous hout..., A. Sampling and DNA extraction
Samples of lake whitefish were collected in 1995-2012 from five locations in Denmark; brackish populations in the Ringkoebing fjord (RIN) and Nissum fjord (NIS), two lagoons connected with the North Sea, and freshwater populations from Lake Flynder (FLYN), Lake Glenstrup (GLEN) and Lake Nors (NORS); and a brackish population from one German location, Achterwasser (ACHT), a lagoon flowing into the Baltic Sea. Houting were collected from the single extant population in Vidaa (VID), a river with outlet into the Wadden Sea (Fig. 1A). Sampling was conducted by electrofishing (VID) and net fishing (remaining populations). Tissue samples consisted of adipose fin clips stored in ethanol at -20°C. DNA was extracted using either a phenol-chloroform method (Taggart et al., 1992) (ACHT, FLYN) or the E.Z.N.A.® Tissue DNA Kit (OMEGA, Bio-tek, CA, USA) following the manufacturer's recommendations (the remaining samples). In total, 35 individuals were whole-genome sequenc..., , # Data from: Genomic insights on conservation priorities for North Sea houting and European Lake whitefish (Coregonus spp.)

[https://doi.org/10.5061/dryad.qfttdz0r0](https://doi.org/10.5061/dryad.qfttdz0r0)

## Description of the data and file structure

The data encompasses multiple VCF files generated from ddRAD and whole-genome sequencing, respectively.

**1) WGS.raw.chr01-40.vcf**\
Raw variant calls from WGS data.

**2) WGS.chr01-40.filtered.collapsed.max2.hw1.miss1.vcf**\
Variant calls from file 1) filtered to discard SNPs out of Hardy Weinberg equilibrium or located in putative duplicated regions. Contains only sites with no missing data.

**3) WGS.chr01-40.ann.filtered.collapsed.max2.hw1.miss1.LD-pruned.vcf**\
An LD-pruned subset of markers from file 2).

**4) WGS.chr01-40.ann.filtered.collapsed.max2.hw1.miss1.phased.vcf**\
Variant calls from file 2) with phase information obtained by statistical phasing with WhatsHap and SHAPEIT4.

**5)** **WGS.chr01-40.filtered.collapsed.max2....