DOI: 10.5061/dryad.6q573n69j
title: Data from: A shift to metapopulation genetic management for persistence of a species threatened by fragmentation: the case of an endangered Australian freshwater fish

description: 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
 depauperate populations can benefit from admixture, and how the outcomes
 of management interventions can be quantified through genetic monitoring.
 We develop the pipeline JeDi (https://github.com/drobledoruiz/JeDi) for
 estimating unbiased individual heterozygosity, population nucleotide
 diversity,y and pairwise population divergence, using
 reduced-representation genome sequencing data and an assembled reference
 genome. We use this pipeline to estimate baseline data for monitoring of
 Macquarie perch populations and show that combining two genetic sources of
 migrants during population restoration resulted in doubling of nucleotide
 diversity compared to either source. Genetic diversity estimates using our
 pipeline are comparable across studies, datasets and species, and suitable
 for evaluating the rate of global biodiversity change.
description: 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
 <em>fastp</em> (Chen et al. 2018), and demultiplexing with
 <em>process_radtags</em> 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 <em>samtools</em> (Li et al. 2009). Genotyping and
 downstream filtering was performed with the pipeline
 <em>JeDi</em>, 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 individual named “ID.bam”, archived as
 .tar.gz, which were used as input for the
 pipeline <em>JeDi</em>.
description: # 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 divergence, using
 reduced-representation genome sequencing data (BAM files) and an assembled
 reference genome (available from [DNA Zoo
 website](https://www.dnazoo.org/assemblies/macquaria_australasica)). ###
 Files and variables #### File: Pavlova-etal-2025_bamfiles.tar.gz
 **Description:** This compressed file is an archive of 719 BAM files for
 719 Macquarie perch *Macquaria australasica* individuals sampled from 20
 populations across the species' range. Use tar with gzip option to
 open the archive. Each BAM file contains single-read sequencing data from
 reduced-representation genome sequencing (DArTseq) mapped onto the
 [chromosomal-length genome
 assembly](https://www.dnazoo.org/assemblies/macquaria_australasica)
 DU_Maus_v1.0_HiC.fasta.gz. #### File: id_pop.txt **Description:** This
 file contains no headers and includes two columns, individual identifier
 and population identifier (assigning each of the 719 individuals to a
 population). ##### Variables * individual ID * population ID ##
 Code/software Raw sequencing reads provided by DArT were pre-processed:
 Illumina adaptors were trimmed with *fastp* (Chen et al. 2018), and
 demultiplexed with *process_radtags* of STACKS package (Catchen et al.
 2013). The processed reads were mapped 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).