Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation

Atlantic sturgeon (Acipenser oxyrinchus ssp. oxyrinchus) has been a food resource in North America for millennia. However, industrial-scale fishing activities following the establishment of European colonies led to multiple collapses of sturgeon stocks, driving populations such as those in the Chesapeake area close to extinction. While recent conservation efforts have been successful in restoring census numbers, little is known regarding genomic consequences of the population bottleneck. Here, we characterise its effect on present-day population structuring and genomic diversity in James River populations. To establish a pre-collapse baseline, we collected genomic data from archaeological remains from Middle Woodland Maycock’s Point (c. 200-900 CE), as well as Jamestown and Williamsburg colonial sites. Demographic analysis of recovered mitogenomes reveals a historical collapse in effective population size, also reflected in diminished present-day mitogenomic diversity and structure. We ..., This dataset comprises the intermediary files obained from bioinformatic processing of raw DNA sequnces obtained through high throughput sequencing of Atlantic sturgeon (AS). Sources of modern AS data: fin clips from James River (Chesapeake DPS) fall and spring populations; Great PeeDee River (South Carolina DPS) fall and spring populations. Sources of archaeological AS data: remains in the form of bones and scutes from Jamestown Colony, Williamsburg Colony and Maycock's point (Middle Woodland site).
Specifically, the datasets produced are based on variants called from target captured exonic DNA and mitogenomes sequenced with the aid of target capture. The population genomic and phylogenomic analytical steps conducted in the publication are outlined here., , # Archaeogenomic analysis of Chesapeake Atlantic sturgeon illustrates shaping of its populations in recovery from severe overexploitation

[https://doi.org/10.5061/dryad.76hdr7t4p](https://doi.org/10.5061/dryad.76hdr7t4p)

This dataset contains files and associated scripts, arranged into 7 sections, corresponding to different analytical processes conducted for the manuscript.  See file `0. READ ME Chesapeake Atlantic Sturgeon workflow` within the zip folder for more details.

## Description of the data and file structure

1\. Alignment files (nuclear and mitochondrial)

2\. Files for ADMIXTURE analysis

3\. PCA and Procrustes PCA - fitting of poorly genotyped ancient samples to population structure analysis

4\. James River fall/spring population assignment tests - testing affinity of ancient samples

5\. Nucleotide diversity estimations for modern samples

6\. Alignments used in phylogenetic and Bayesian Skyline analyses

7\. (Supplementary) files used for currentNe

## Sharing/Access ...

大西洋鲟（Atlantic sturgeon，学名*Acipenser oxyrinchus ssp. oxyrinchus*）数千年来一直是北美地区的食物资源。然而，欧洲殖民地建立后兴起的工业化捕捞活动导致鲟鱼种群多次崩溃，切萨皮克湾等区域的种群濒临灭绝。尽管近期的保护工作成功恢复了普查种群数量，但人们对种群瓶颈带来的基因组后果仍知之甚少。本研究聚焦其对詹姆斯河种群当前群体结构与基因组多样性的影响。为建立捕捞前的基线数据，我们采集了中林地时期梅科克角遗址（约公元200-900年）以及詹姆斯敦、威廉斯堡殖民遗址的考古遗存基因组数据。对已获取的线粒体基因组的群体遗传学分析显示，历史上有效种群大小曾发生崩溃，这一特征也体现在当代线粒体基因组多样性与结构的降低上。……

本数据集包含通过对大西洋鲟（简称AS）进行高通量测序获得的原始DNA序列经生物信息学处理后得到的中间文件。现代大西洋鲟数据来源：詹姆斯河（切萨皮克湾独特种群单元（DPS））秋季与春季种群的鳍剪样本；皮迪大河（南卡罗来纳州独特种群单元）秋季与春季种群的鳍剪样本。考古大西洋鲟数据来源：詹姆斯敦殖民地、威廉斯堡殖民地以及梅科克角（中林地时期遗址）出土的骨骼与骨板遗骸。本数据集基于目标捕获的外显子DNA与线粒体基因组的变异检测结果构建，论文中开展的群体基因组学与系统基因组学分析步骤在此概述。

# 切萨皮克湾大西洋鲟的古基因组分析揭示其在严重过度开发后的种群恢复历程
[https://doi.org/10.5061/dryad.76hdr7t4p](https://doi.org/10.5061/dryad.76hdr7t4p)

本数据集包含文件与配套脚本，分为7个模块，对应论文中开展的不同分析流程。详见压缩包内的`0. READ ME Chesapeake Atlantic Sturgeon workflow`文件以了解更多细节。

## 数据与文件结构说明
1. 比对文件（核基因组与线粒体基因组）
2. ADMIXTURE分析文件
3. 主成分分析（Principal Component Analysis，简称PCA）与普氏PCA（Procrustes PCA）——将基因型缺失严重的古代样本拟合至群体结构分析
4. 詹姆斯河秋季/春季种群归属检验——验证古代样本的群体亲缘关系
5. 现代样本的核苷酸多样性评估
6. 系统发育与贝叶斯天际线分析所用的比对文件
7. （补充）currentNe分析所用的文件

## 共享与获取……