Multifaceted framework for defining conservation units: An example from Atlantic salmon (Salmo salar) in Canada

Conservation units represent important components of intraspecific diversity that can aid in prioritizing and protecting at-risk populations, while also safeguarding unique diversity that can contribute to species resilience. In Canada, identification and assessments of conservation units are done by the Committee on the Status of Endangered Wildlife in Canada (COSEWIC). COSEWIC can recognize conservation units below the species level (termed “designatable units”; DUs) if the unit has attributes that make it both discrete and evolutionarily significant. There are various ways in which a DU can meet the criteria of discreteness and significance, and increasing access to “big data” is providing unprecedented information that can directly inform both criteria. Specifically, the incorporation of genomic data for an increasing number of non-model species is informing more COSEWIC assessments; thus, a repeatable, robust framework is needed for integrating these data into DU characterization. ..., Genomic data here includes data used for Labrador, Canada, in the main analysis of the paper. Genomic data from a 220,000 SNP array (see Barson et al., 2015) developed using a targeted, biallelic SNP Affymetrix Axiom array by the Centre for Integrative Genetics (CIGENE, Ås, Norway) were compiled for populations of Atlantic salmon. Genotyping was performed using the Affymetrix Axiom array protocol (Thermo Fisher Scientific), with raw data processed using the Axiom Analysis Suite (AAS) software based on the manufacturer's best practices protocol. AAS assigns all SNP assays into different categories based on clustering patterns, and only SNPs that were classified as high quality were used for subsequent analyses. SNPs were filtered using PLINK v1.9 (Purcell et al., 2007) for minor allele frequency (MAF) of 0.05., , # Multifaceted framework for defining conservation units: An example from Atlantic salmon (*Salmo salar*) in Canada

[https://doi.org/10.5061/dryad.6wwpzgn4h](https://doi.org/10.5061/dryad.6wwpzgn4h)

## Description of the data and file structure

Data are in plink format (.fam, .bim, .bed), see plink website for full details of formatting [https://www.cog-genomics.org/plink/1.9/formats](https://www.cog-genomics.org/plink/1.9/formats)

### Files and variables

#### File: Labrador\_220K\_maf005.fam

**Description:** plink .fam file for SNP dataset, which includes ID and population information

#### File: Labrador\_220K\_maf005.bed

**Description:** plink .bed file for SNP dataset, which includes genotype data

#### File: Labrador\_220K\_maf005.bim

**Description:** plink .bim file for SNP dataset, which includes all SNP position information (map)

## Code/software

Codes used for the manuscript are provided at: [https://github.com/SarahLehnert/Salmon_DUs](https://github.com/SarahLehnert/...,

保护单元（conservation units）是种内多样性的重要组成部分，有助于优先识别并保护受威胁种群，同时亦可保护有助于提升物种恢复力的独特多样性。在加拿大，保护单元的鉴定与评估工作由加拿大濒危野生动物状况委员会（Committee on the Status of Endangered Wildlife in Canada, COSEWIC）负责开展。若某一单元兼具离散性与进化显著性特征，COSEWIC可将其认定为物种级以下的保护单元，即“可指定单元（designatable units, DUs）”。可指定单元满足离散性与进化显著性标准的途径多样，而“大数据”获取门槛的不断降低正为两类标准的判定提供前所未有的精准信息。具体而言，针对越来越多非模式物种的基因组数据正被更多地应用于COSEWIC的评估工作，因此亟需一套可重复、高鲁棒性的分析框架，将此类数据整合至可指定单元的特征界定流程中。
本研究的基因组数据涵盖本文主要分析中使用的加拿大拉布拉多地区样本数据。本研究针对大西洋鲑鱼种群整合了由挪威奥斯Ås的整合遗传学中心（Centre for Integrative Genetics, CIGENE）基于靶向双等位基因单核苷酸多态性（single nucleotide polymorphism, SNP）Affymetrix Axiom芯片开发的22万SNP芯片（详见Barson等人，2015年）所产生的基因组数据。基因分型实验采用赛默飞世尔科技（Thermo Fisher Scientific）的Affymetrix Axiom芯片实验流程完成，原始数据则依据厂商官方最佳操作流程，通过Axiom分析套件（Axiom Analysis Suite, AAS）软件进行处理。AAS软件会基于聚类模式将所有SNP检测分为不同类别，仅将归类为高质量的SNP用于后续分析。本研究使用PLINK v1.9（Purcell等人，2007年）对SNP进行过滤，保留次要等位基因频率（minor allele frequency, MAF）≥0.05的位点。

# 界定保护单元的多维度框架：以加拿大大西洋鲑鱼（*Salmo salar*）为例
https://doi.org/10.5061/dryad.6wwpzgn4h

## 数据与文件结构说明
数据采用PLINK格式（.fam、.bim、.bed），格式细节可参考PLINK官方网站：https://www.cog-genomics.org/plink/1.9/formats

### 文件与变量说明
#### 文件：Labrador_220K_maf005.fam
**说明：** 该文件为SNP数据集的PLINK .fam文件，包含样本ID与种群信息

#### 文件：Labrador_220K_maf005.bed
**说明：** 该文件为SNP数据集的PLINK .bed文件，包含基因型数据

#### 文件：Labrador_220K_maf005.bim
**说明：** 该文件为SNP数据集的PLINK .bim文件，包含所有SNP位点的位置信息（即遗传图谱）

## 代码与软件
本文手稿所用代码已上传至：https://github.com/SarahLehnert/Salmon_DUs