Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation

Management interventions for threatened species are well documented with genetic data now playing a pivotal role in informing their outcomes. However, in situ actions, such as supplementations (the release of individuals into an existing population of conspecifics) are often restricted to a single site to advise species-level management decisions. A considerable amount of research and management effort has been dedicated to conserving the endangered Tasmanian devil (Sarcophilus harrisii), offering a unique opportunity to investigate the temporal genetic consequences of supplementation at multiple sites, in comparison to outcomes observed in the absence management interventions. Using 1,778 genome-wide SNPs across 1,546 individuals, we compared four wild supplemented sites to four monitoring-only sites (not supplemented; control sites) over nine years (2014-2022). By the end of the study, genetic differentiation among supplemented sites had significantly decreased compared to among not-s..., There is once dataset included in the Excel workbook:
A set of SNPs generated using DArTSeq, a form of reduced representation sequencing. Genotype SNP data were quality filtered using the dartR package (v 2.9.7) in Rstudio (v 4.3.1). We filtered out monomorphic loci and SNPs with low (lower threshold = 5) and high (upper threshold) mean read counts. Further filtered on a reproducibility of ≥95%, loci with a call rate of ≥70%, 0.001 minor allele frequency, individual call rate of ≥70%. Loci were filtered out if the SNP position was outside the trimmed sequence tag, secondary SNPs in the same sequence, or predicted to be sex linked. Data was subset to include individuals for the current study, monomorphic loci were removed here and refiltered with a call rate of ≥70%., , # Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation

[https://doi.org/10.5061/dryad.j3tx95xqr](https://doi.org/10.5061/dryad.j3tx95xqr)

## Description of the data and file structure

##### General Information

* Title of dataset 
* Data to: Temporal changes in Tasmanian devil genetic diversity at sites with and without supplementation.
* Author information (principal investigator)
* Name: Prof. Carolyn Hogg
* Institution: The University of Sydney
* Email: [[e-mail]](mailto:[e-mail])
* Dates of data collection
* 2014 to 2022 
* Geographic location of data collection
* Tasmanian devil wild sites, Tasmania Australia.
* Information about funding sources.
* The Australian Research Council (LP180100244), The University of Sydney, Save the Tasmanian Devil Program and the San Diego Zoo Wildlife Alliance.

##### Sharing/Access Information

* Links to publications that cite or use data
* Andrea L. S...

针对濒危物种的管理干预措施已有大量文献记载，如今遗传数据在阐释干预成效方面发挥着关键作用。然而，诸如种群补充（将个体放归至现有同物种种群中）这类原位保护行动，通常仅局限于单个站点，用于指导物种类别的管理决策。针对濒危袋獾（*Sarcophilus harrisii*）的保护研究与管理投入已相当可观，这为我们提供了独特的研究契机：对比无管理干预情况下的观测结果，探究多站点种群补充的时间尺度遗传效应。本研究基于1546个个体的1778个全基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点，对9年间（2014-2022年）的4个野生种群补充站点与4个仅监测站点（未开展种群补充，即对照站点）进行了对比分析。截至研究结束时，种群补充站点间的遗传分化程度较未补充站点间出现了显著下降（原文此处未完整）。

本研究数据集包含于Excel工作簿中：
采用DArTSeq（一种简化代表性测序技术）生成的单核苷酸多态性位点数据集。在RStudio（v4.3.1）中使用dartR软件包（v2.9.7）对基因型SNP数据进行质量过滤：首先剔除单态位点以及平均读段数过低（下限阈值=5）和过高的SNP位点；进一步基于以下标准过滤：重复性≥95%、位点分型成功率≥70%、次要等位基因频率≥0.001、个体分型成功率≥70%；同时剔除位于修剪后序列标签之外的SNP位点、同一序列中的次级SNP位点，以及预测为性连锁的位点。本研究子集仅纳入当前研究所需的个体，同时剔除单态位点并以分型成功率≥70%为标准再次过滤。

# 有/无种群补充站点的袋獾遗传多样性时间变化
[https://doi.org/10.5061/dryad.j3tx95xqr](https://doi.org/10.5061/dryad.j3tx95xqr)

## 数据与文件结构说明

### 基本信息
* 数据集标题
* 数据集主题：有/无种群补充站点的袋獾遗传多样性时间变化
* 作者信息（首席研究员）
* 姓名：Carolyn Hogg教授
* 所属机构：悉尼大学
* 电子邮箱：[e-mail]
* 数据采集时间
* 2014年至2022年
* 数据采集地理区域
* 澳大利亚塔斯马尼亚州袋獾野生监测站点
* 资助来源信息
* 澳大利亚研究理事会（LP180100244）、悉尼大学、拯救袋獾项目以及圣地亚哥动物园野生动物联盟

### 共享/获取信息
* 引用或使用本数据集的出版物链接
* Andrea L. S...