Data for: Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia

Genomic diversity is a fundamental component of Earth’s total biodiversity and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species’ range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the ...,

We used next-generation sequencing data from remnant populations of the threatened black-footed tree-rat (Mesembriomys gouldii) to compare patterns of genomic diversity and differentiation across the landscape and investigate genomic diversity metrics to better understand brush-tailed rabbit-rat population genomic structure. We also ran a quantitative prioritisation analysis to determine which populations are the most cost-effective to conserve for the retention of genomic diversity. Detailed methods are provided in the published manuscript.
All bioinformatic and R scripts are provided as part of the dataset. All relevant input and output files for ANGSD, SNeP and STACKS, as well as filtered genotypes, are provided.

, Software used for this publication/dataset include the following. However, many different software programs can be used to open the files and run the same or similar analyses.
R
STACKS
BWA
SAMTOOLS
ANGSD
SNeP
PLINK
TreeMix
MARXAN

基因组多样性（genomic diversity）是地球总生物多样性（biodiversity）的核心组成部分，在生物多样性保护工作中需予以明确考量。若要保护基因组多样性，必须对其空间分布进行测定，并量化任意种内进化谱系（intraspecific evolutionary lineages）对整体基因组多样性的贡献。本研究针对受威胁的澳洲啮齿类动物——黑足树鼠（*Mesembriomys gouldii*），描述了其全分布范围的种群基因组结构，旨在为长期监测数据匮乏的大型区域内种群衰退的时间与程度提供研究视角。通过估算4个采样点的近期有效种群大小（effective population sizes）动态变化轨迹，我们证实该物种分布范围内普遍存在种群衰退现象，但发现达尔文地区城郊区域的种群相对更为稳定。基于当前采样数据，梅尔维尔岛（Melville Island）种群对整体等位基因丰富度（allelic richness）的贡献最大……

本研究利用受威胁的黑足树鼠残存种群的下一代测序（next-generation sequencing）数据，对比分析了全景观尺度下的基因组多样性与分化模式，并通过基因组多样性指标探究，以更深入解析刷尾兔鼠（brush-tailed rabbit-rat）的种群基因组结构。此外，我们还开展了定量优先级分析，以确定哪些种群在保留基因组多样性方面具有最高的成本效益保护价值。详细的研究方法已发表于相关学术论文中。

本数据集附带所有生物信息学脚本与R脚本。ANGSD、SNeP与STACKS分析所需的全部相关输入、输出文件，以及过滤后的基因型数据均已随数据集提供。

本出版物/数据集所使用的软件如下。不过，诸多其他软件亦可用于打开相关文件并运行同类或相似分析：
R
STACKS
BWA
SAMTOOLS
ANGSD
SNeP
PLINK
TreeMix
MARXAN