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Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program

Citation

McLennan, Elspeth et al. (2022), Restoring faith in conservation action: maintaining wild genetic diversity through the Tasmanian devil insurance program, Dryad, Dataset, https://doi.org/10.5061/dryad.2bvq83bsm

Abstract

Conservation breeding programs aim to maintain 90% wild genetic diversity, but rarely assess functional diversity. Here, we compare both genome-wide and functional diversity (in over 500 genes) of Tasmanian devils (Sarcophilus harrisii) within the insurance metapopulation and across the species’ range (64,519 km2). Populations have declined by 80% since 1996 due to a contagious cancer, devil facial tumour disease (DFTD). However, predicted local extinctions have not occurred. Recent suggestions of selection for “resistance” alleles in the wild precipitated concerns that insurance population devils may be unsuitable for translocations. Using 830 wild samples collected at 31 locations between 2012-2021, and 553 insurance metapopulation devils, we show that the insurance metapopulation is representative of current wild genetic diversity. Allele frequencies at DFTD-associated loci were not substantially different between captive and wild devils. Methods presented here are valuable for others investigating evolutionary potential in threatened species, particularly ones under significant selective pressures.

Methods

There are three datasets included here:

1. A set of SNPs generated using DArTseq, a form of reduced representation sequencing. The raw files were cleaned, aligned to the Tasmanian devil reference genone, and a catalogue of consitent SNPs were called using STACKS. The SNP set was further filtered in R using the following parameters of 2.5x read depth, 80% call rate, 90% reproducibility based on technical replicates, 0.001 minor allele frequency and a maximum heterozygosity of 70%.

2. A set of SNPs generated using a custom target capture approach to assess functional diversity in the Tasmanian devil. The custom probe set was deisgned to capture three categories of sequence targes: 1) immune genes, 2) reproductive genes, and 3) DFTD-associated loci. Raw reads were aligned to the Tasmanian devil reference genome using BWA and variant calling and filtering was performed in GATK. Linked SNPs were pruned using SNPRelate R package.

3. The same SNP set generated in step 2 but without the linkage pruning.

Funding

Toledo Zoo and Aquarium

Australian Research Council, Award: LP180100244

Save the Tasmanian Devil Program

San Diego Zoo and Wildlife Alliance