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 remove indels, monomorphic sites, multi-allelic SNPs and SNPs with a variant quality <20 or extreme depth of coverage (lower than 400 or higher than 1000 across all individuals) and 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.mis...,

种群基因组学分析对于濒危种群的保护决策具有重要指导价值。本研究聚焦于极具争议的欧洲白鲑（Coregonus spp.）种群案例。濒危的北海南鳟是唯一一种能耐受海洋盐度的白鲑科鱼类，此前被认为是与欧洲湖白鲑（C. lavaretus）独立的物种（C. oxyrhinchus）。然而，目前尚无确凿证据表明其存在基于遗传的盐度适应性。此外，基于微卫星和线粒体基因组数据的研究显示，南鳟与湖白鲑的分化时间惊人地晚，仅约2500年前（bp，即距今）。且上述两类数据均未发现其存在近交的迹象。最后，近期一项颇具争议的分类学修订将该区域所有白鲑均归为C. maraena，这使得南鳟的保护优先级受到了质疑。本研究采用全基因组测序与双酶切限制性位点相关DNA测序（ddRAD）技术，对6个湖白鲑种群以及仅存的本土南鳟种群[原文此处截断]进行了分析。

A. 采样与DNA提取
湖白鲑样本于1995-2012年间采自丹麦5处采样点：分别是与北海相连的两处潟湖——林克平湾（Ringkoebing fjord, RIN）与尼苏姆湾（Nissum fjord, NIS）的咸淡水种群，以及弗林德湖（Lake Flynder, FLYN）、格伦斯特鲁普湖（Lake Glenstrup, GLEN）与诺斯湖（Lake Nors, NORS）的淡水种群；此外还采自德国一处采样点阿赫特瓦瑟湾（Achterwasser, ACHT）——一处流入波罗的海的潟湖的咸淡水种群。南鳟样本采自其唯一现存种群维达河（Vidaa, VID），该河最终注入瓦登海（图1A）。采样方式包括电渔法（维达河种群）与网捕法（其余种群）。组织样本取自脂鳍，保存于-20℃的乙醇中。DNA提取分别采用酚-氯仿法（Taggart等，1992）（对应ACHT、FLYN样本）与E.Z.N.A.®组织DNA提取试剂盒（OMEGA，Bio-tek，美国加利福尼亚州），后者严格遵循制造商说明书操作（其余样本）。总计35个个体完成了全基因组测序[原文此处截断]。

# 数据来源：《北海南鳟与欧洲湖白鲑（Coregonus spp.）保护优先级的基因组学解析》
https://doi.org/10.5061/dryad.qfttdz0r0

## 数据与文件结构说明
本数据集包含分别由ddRAD测序与全基因组测序获得的多个变异位点调用格式（VCF）文件。

**1) WGS.raw.chr01-40.vcf**
全基因组测序数据的原始变异位点调用结果。

**2) WGS.chr01-40.filtered.collapsed.max2.hw1.miss1.vcf**
对文件1的变异位点进行过滤后的结果，过滤规则包括移除插入缺失位点、单态位点、多等位基因单核苷酸多态性（Single Nucleotide Polymorphism, SNPs）、变异质量值低于20的SNPs、覆盖度极端（所有个体覆盖度低于400或高于1000）的SNPs，以及偏离哈迪-温伯格平衡或位于推测重复区域的SNPs；该文件仅包含无缺失数据的位点。

**3) WGS.chr01-40.ann.filtered.collapsed.max2.hw1.miss1.LD-pruned.vcf**
对文件2的标记进行连锁不平衡（LD）修剪后的子集。

**4) WGS.chr01-40.ann.filtered.collapsed.max2.hw1.mis... [原文此处截断]