Data from: Heterogeneous patterns of heterozygosity loss in isolated populations of the threatened eastern barred bandicoot (Perameles gunnii)
Data files
Dec 16, 2023 version files 20.75 GB
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EBB_10x-rails.scaffolds_50K.fa
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metadata.csv
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README.md
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Abstract
Perameles gunnii is an endangered terrestrial marsupial on mainland Australia, but comparitively widespread in Tasmania. No research has yet aimed to assess population structure or genetic diversity in this state until now, where we assess genomic similarity and diversity using a ddRAD dataset of 117 Tasmanian animals.
First, we assigned all samples to populations (or demes), according to their coordinate metadata and known geographic boundaries. We then test this hypothesis with population-ignorant genetic clustering analyses: PCA, Structure, and fineRADstructure. Validating seven (7) populations, four in a distinct "northern" group and three in a "southern" groupd, and also identify two populations displaying significant and unexpected isolation. We then looked to directly assess migration between these populations find little evidence, although genetic similarity within nothern and southern groups suggests that gradual mixing is ongoing within these areas.
We assessed autosomal heterozygosity of individuals using a custom bioinformatic pipeline, and use a Kriging approach to plot regions of Tasmania where higher and lower heterozygosity individuals occur, finding unequal distribution of heterozygosity across geographic barriers that did not appear to affect genetic similarit-based analyses, potentially indicating emerging substructure within populations. We found individual heterozygosities varied within demes by up to a factor of two, and demes with low heterozygosity individuals also still contained those with high heterozygosity.
Our results provide novel insights into the relationship between isolation-driven genetic structure and local heterozygosity patterns. These may help improve translocation efforts, by identifying populations in need of assistance, and by providing an individualized metric for identifying source animals for translocation.
README: Perameles gunnnii Tasmania 2008-2011
https://doi.org/10.5061/dryad.ksn02v7b0
Genotypic data and metadata for 117 Tasmanian Perameles gunnii, sampled from the wild between 2008-2011, and 17 Victorian Perameles gunnii from Mt Rothwell Biodiversity Interpretation Centre, sampled from 2016.
Samples provided as demultiplexed raw reads in .fq.gz format, and a draft scaffold genome is provided in .fa format.
Metadata contains incomplete 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, and whether coordinates are exact or approximate is indicated in the metadata. Metadata also contains incomplete sex data; where sex was unknown, NA has been used to indicate this.
Additionally, publicly available, post-1990 sighing data for P. gunnii in Tasmania is available in ALA. Also, the distribution map figure that was generated using this data is available in the manuscript related to this repository.
Description of the data and file structure
Processing details for the raw reads and draft 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/t-ludovic-schmidt/autosomal_het/