A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish

In a world where habitats are degrading and the climate is warming and becoming unpredictable, biodiversity conservation efforts and funding remain grossly inadequate. As part of a multi-faceted approach to halting extinctions, shifting from preserving small, remnant populations to a practice of genetically connecting populations that recreate larger and more diverse populations is expected to be beneficial. This harnesses key evolutionary processes to promote species’ abilities to adapt to changing environments and to increase the likelihood of population persistence. We use the endangered Macquarie perch (Macquaria australasica) as a case study to develop a genetic strategy for metapopulation management aimed at promoting population growth and persistence. The Macquarie perch’s range has been highly fragmented, and its remaining habitat is at risk of catastrophic degradation due to climate change. We integrate results of new and existing genetic analyses to illustrate how genetically ..., To obtain data for variant and invariant sites for all individuals, we used raw sequencing data provided by DArT. Pre-processing of raw reads included trimming Illumina adaptors with fastp (Chen et al. 2018), and demultiplexing with process_radtags of STACKS package (Catchen et al. 2013). We mapped the processed reads to the chromosome-length Macquarie perch genome using BWA-MEM (Li and Durbin 2009) with parameter -R set to '@RG\tID:sample_name\tSM:sample_name'. Mapped reads per individual were sorted, filtered (min MAPQ ≥ 20) and transformed to BAM with samtools (Li et al. 2009). Genotyping and downstream filtering was performed with the pipeline JeDi, resulting in a dataset of 706 individuals scored for 8,236,685 total sites, including 51,900 variant sites (including 46,973 biallelic and 4,927 tri- or tetra-allelic).
This dataset includes 1) a tab-separated file with the first column being individual IDs, and the second column their population, 2) mapped reads in a BAM file per indivi..., # A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish

Dataset DOI: [10.5061/dryad.6q573n69j](10.5061/dryad.6q573n69j)

## Description of the data and file structure

This repository contains genomic data for the manuscript:

Pavlova, A., Tonkin, Z., Pearce, L., Robledo-Ruiz, D., Lintermans, M., Ingram, B., Lyon, J., Beitzel, M., Broadhurst, B., Rourke, M., Sturgiss, F., Lake, E., Castrejón-Figueroa, J., Stocks, J., & Sunnucks, P. (2025). A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish. *Molecular Ecology*. DOI:10.1111/mec.70005, accepted 5/6/2025.

The two files in this repository could be used as input for *JeDi* pipeline described in the manuscript. The JeDi pipeline estimates unbiased individual heterozygosity, population nucleotide diversity and pairwise population divergen...,

在栖息地持续退化、气候变暖且日趋不可预测的当下，全球生物多样性保护工作与资金投入仍严重不足。作为遏制物种灭绝的多维度防控策略之一，将保护范式从维持小型残存种群，转向通过遗传连接各离散种群以重建更大、更多样化种群的实践路径，有望带来显著效益。该策略依托核心进化过程，可提升物种应对环境变化的适应能力，并增强种群长期存续的概率。我们以濒危物种麦夸里鲈（Macquaria australasica）为案例研究对象，开发了一套面向集合种群（metapopulation）管理的遗传策略，旨在推动种群增长与存续。麦夸里鲈的自然分布范围已高度破碎化，其残存栖息地因气候变化面临灾难性退化的风险。我们整合全新与已有遗传分析的结果，以阐明遗传... 为获取所有个体的变异位点与单态位点数据，我们采用了DArT提供的原始测序数据。原始测序reads的预处理流程包括：使用fastp（Chen等，2018）裁剪Illumina接头序列，以及借助STACKS软件包的process_radtags工具完成解复用。随后，我们使用BWA-MEM（Li与Durbin，2009）将处理后的reads比对至染色体水平的麦夸里鲈参考基因组，比对参数-R设置为`@RG ID:sample_name SM:sample_name`。对每个个体的比对reads进行排序、过滤（最低MAPQ值≥20），并通过samtools（Li等，2009）转换为BAM格式文件。后续通过JeDi分析流程完成基因分型与精细化过滤，最终得到涵盖706个个体的数据集，共检测8,236,685个位点，其中包含51,900个多态变异位点（含46,973个双等位基因位点与4,927个三/四等位基因位点）。

本数据集包含：1）制表符分隔的文本文件，第一列为个体ID，第二列为其所属种群；2）每个个体对应的比对reads的BAM格式文件（原文后续内容省略）...

# 转向集合种群遗传管理以保护受生境破碎化威胁的物种：以澳大利亚濒危淡水鱼类为例

数据集DOI：[10.5061/dryad.6q573n69j](10.5061/dryad.6q573n69j)

## 数据与文件结构说明

本仓库包含对应学术论文的基因组数据：Pavlova, A.、Tonkin, Z.、Pearce, L.、Robledo-Ruiz, D.、Lintermans, M.、Ingram, B.、Lyon, J.、Beitzel, M.、Broadhurst, B.、Rourke, M.、Sturgiss, F.、Lake, E.、Castrejón-Figueroa, J.、Stocks, J. 与 Sunnucks, P.（2025）。《转向集合种群遗传管理以保护受生境破碎化威胁的物种：以澳大利亚濒危淡水鱼类为例》，发表于*Molecular Ecology*，DOI:10.1111/mec.70005，2025年6月5日被接收。

本仓库内的两个文件可作为论文中所述*JeDi*分析流程的输入文件。*JeDi*流程可估算无偏个体杂合度、种群核苷酸多样性及种群间成对分化水平（原文后续内容省略）...