Exome capture of Antarctic krill (Euphausia superba) for cost effective genotyping and population genetics with historical collections

Antarctic krill (Euphausia superba Dana) is a keystone species in the Southern Ocean ecosystem, with ecological and commercial significance. However, its vulnerability to climate change requires an urgent investigation of its adaptive potential to future environmental conditions. Historical museum collections of krill from the early 20th century represent an ideal opportunity to investigate how krill have changed over time due to predation, fishing, and climate change. However, there is currently no cost-effective method for implementing population scale collection genomics for krill given its genome size (48Gbp). Here, we assessed the utility of two inexpensive methods for population genetics using historical krill samples, specifically low-coverage shotgun sequencing (i.e., “genome-skimming”) and exome capture. Two full-length transcriptomes were generated and used to identify 166 putative gene targets for exome capture bait design. A total of 20 historical krill samples were sequence..., , , # Exome capture of Antarctic krill (*Euphausia superba*) for cost effective genotyping and population genetics with historical collections.

[https://doi.org/10.5061/dryad.v6wwpzh4p](https://doi.org/10.5061/dryad.v6wwpzh4p)

## Description of the data and file structure

This data includes the configuration files and reference data used for the analyses of genome skimming data from krill museum collections. In addition, mitochondrial and ribosomal sequences assembled from previously published raw sequence data are shared here. Finally, sankey plots to visualise where sequence data was retained or lost throughout each step of the pipeline are presented.  

### Files and variables

#### File: gene2phylo\_config.yaml

**Description:** Configuration file for the gene2phylo pipeline used in this study. This YAML file contains all parameter settings and input specifications required to reproduce the phylogenetic analyses presented in the paper. Key configuration options include input directo...,

南极磷虾（*Euphausia superba Dana*）是南大洋生态系统的关键物种，兼具生态与商业价值。然而其对气候变化的脆弱性，使得亟需探究其对未来环境条件的适应潜力。20世纪早期留存的南极磷虾博物馆馆藏样本，为研究磷虾因捕食、捕捞及气候变化产生的长期变化提供了理想契机。但鉴于南极磷虾基因组规模达48Gbp，目前尚无经济高效的种群尺度群体基因组学研究方法。本研究针对馆藏磷虾样本，评估了两种低成本群体遗传学研究方法的实用性：低覆盖度鸟枪测序（low-coverage shotgun sequencing），即“基因组浅层测序（genome-skimming）”，与外显子组捕获（exome capture）。我们构建了两个全长转录组（transcriptome），并以此为基础鉴定出166个候选基因靶点用于外显子组捕获探针设计。本研究共获取20份馆藏磷虾样本的序列数据……， , , # 基于馆藏样本的南极磷虾（*Euphausia superba*）外显子组捕获：实现低成本基因分型与群体遗传学研究

[https://doi.org/10.5061/dryad.v6wwpzh4p](https://doi.org/10.5061/dryad.v6wwpzh4p)

## 数据与文件结构说明
本数据集包含用于分析磷虾馆藏样本基因组浅层测序数据的配置文件与参考数据集。此外，本数据集还共享从已发表原始测序数据中组装得到的线粒体与核糖体序列。最后，本数据集提供桑基图（Sankey plots），用于可视化展示测序数据在分析流程各步骤中的留存与丢失情况。

### 文件与变量
#### 文件：gene2phylo_config.yaml
**描述**：本研究中使用的gene2phylo分析流程配置文件。该YAML格式文件包含复现论文中系统发育分析所需的全部参数设置与输入规范，核心配置选项包括输入目录……