DOI: 10.5061/dryad.34tmpg4v3
title: Simulating genetic mixing in strongly structured populations of the threatened southern brown bandicoot (Isoodon obesulus)

description: Genetic mixing aims to increase the genetic diversity of small or isolated
 populations, by mitigating genetic drift and inbreeding depression, either
 by maximally increasing genetic diversity, or minimising the prevalence of
 recessive, deleterious alleles. However, few studies investigate this
 beyond a single generation of mixing. Here, we model the mixing using
 captive, low diversity recipient population of the threatened Southern
 brown bandicoot (Isoodon obesulus) over fifty generations, and compare
 wild populations across south-eastern Australia as candidate source
 populations. We first assess genetic differentiation between twelve
 populations, including the first genomic assessment of three mainland
 Australian and three Tasmanian populations. We assess genetic diversity in
 the twelve populations using a novel autosomal heterozygosity pipeline,
 using these results to identify a candidate recipient population for
 genetic mixing simulations. We found that populations fell into four major
 groups of genetic similarity: Adelaide Hills, western Victoria, eastern
 Victoria, and Tasmania, but populations within these groups were also
 distinct, and additional substructure was observed in some populations.
 Our autosomal heterozygosity pipeline indicated significant variability in
 mean heterozygosity between populations, identifying one extremely
 genetically degraded population on Inner Sister Island, Tasmania. Genetic
 mixing simulations of a low heterozygosity captive population in Victoria
 suggested the greatest increase in heterozygosity would be reached by
 using highly differentiated populations as mixing sources. However, when
 removing outlying populations with extreme differentiation, neither
 metrics of differentiation nor heterozygosity were strongly correlated
 with modelled heterozygosity increase, indicating the value of
 simulation-based approaches when selecting source populations for
 population mixing.
description: # Simulating genetic mixing in strongly structured populations of the
 threatened southern brown bandicoot (Isoodon obesulus)
 [https://doi.org/10.5061/dryad.34tmpg4v3](https://doi.org/10.5061/dryad.34tmpg4v3) ## Description of the data and file structure Genotypic data and metadata for 185 *Isoodon obesulus*, sampled from wild and captive sites across south-eastern between 2008-2023. Samples provided as demultiplexed raw reads in .fq.gz format, with barcode, metadata, and pop-map files. Metadata contains coordinate data approximated to two (2) decimal places to protect a sensitive species, as per The Global Biodiversity Information Facility (Category 3 sensitive species). Where exact coordinate data was unavailable, approximate data was inferred from the recorded locality. Two samples had broad location metadata, but no recorded coordinates or locality; coordinates for these samples are recorded as "n/a". Metadata also contains incomplete sex data; where sex was unknown, "n/a" has been used to indicate this. Three replicate samples are included, indicated by A or B as the final character: WP01A/B, CRBG_02A/B, MR23A/B. Figure 1 in the paper has been generated from publicly available, 1990-2023 observation data for *I. obesuslus* stored in ALA. This data is not CC-0 and thus cannot be uploaded directly to Dryad, but is readily accessible.  ### Description of the data and file structure Processing details for the raw reads and pseudo-genome are in the associated manuscript.\ All programs used to process data, including version, are also indicated in the manuscript.\ All software used is open source. ### Code/Software This manuscript uses an autosomal heterozygosity pipeline available at [https://github.com/jblack222/AutoHet](https://github.com/jblack222/AutoHet) This manuscript uses population mixing simulations, available at [https://github.com/jblack222/SimIntro](https://github.com/jblack222/SimIntro) ### Files and variables #### File: README.txt **Description:** This file is a brief description of other files in the repository. #### File: SBB\_barcodes.txt **Description:** This file is two columns, tab-seperated, containing sample ID and associated barcode for demultiplexing. ##### Variables * ID * Barcode #### File: SBB\_popmap.txt **Description:** This file is two columns, tab-seperated, containing sample ID and associated population for downstream analysis. ##### Variables * ID * Location #### File: demultiplexed\_data.tar.gz **Description:** This is a tar-ball directory containing 185 demultiplexed raw genomic data files for samples, in .fastq.gz format.  #### File: SBB\_metadata.csv **Description:** This file contains all relevant metadata for replication of this study. ##### Variables * ID: * Location: * Region: * Lat: * Long: * Sex: ## Code/software All software used in the manuscript are open source, freely accessible, and clearly described in the text, except those specified below which were developed for the manuscript. **Individual Autosomal Heterozygosity analysis:** This code, as described in the manuscript, is for a novel calculation of heterozygosity. Code for generating individual estimates for heterozygosity is available at https://github.com/jblack222/AutoHet **Simulated Introductions analysis** This code, as described in the manuscript, is for calculation of heterozygosity change after mixing of populations. Code for generating individual estimates for heterozygosity is available athttps://github.com/jblack222/SimIntro ## Access information Data used for Figure 1B was derived from the Atlas of Living Australia, https://www.ala.org.au/