DOI: 10.5061/dryad.m8297
title: Data from: Lack of genetic diversity across diverse immune genes in an endangered mammal, the Tasmanian devil (Sarcophilus harrisii)

description: The Tasmanian devil (Sarcophilus harrisii) is threatened with extinction
 due to the spread of devil facial tumour disease. Polymorphisms in immune
 genes can provide adaptive potential to resist diseases. Previous studies
 in diversity at immune loci in wild species have almost exclusively
 focused on genes of the major histocompatibility complex (MHC); however,
 these genes only account for a fraction of immune gene diversity. Devils
 lack diversity at functionally important immunity loci, including MHC and
 Toll-like receptor genes. Whether there are polymorphisms at devil immune
 genes outside these two families is unknown. Here, we identify
 polymorphisms in a wide range of key immune genes, and develop assays to
 type single nucleotide polymorphisms (SNPs) within a subset of these
 genes. A total of 167 immune genes were examined, including cytokines,
 chemokines and natural killer cell receptors. Using genome-level data from
 ten devils, SNPs within coding regions, introns and 10 kb flanking genes
 of interest were identified. We found low polymorphism across 167 immune
 genes examined bioinformatically using whole-genome data. From this data,
 we developed long amplicon assays to target nine genes. These amplicons
 were sequenced in 29–220 devils and found to contain 78 SNPs, including
 eight SNPS within exons. Despite the extreme paucity of genetic diversity
 within these genes, signatures of balancing selection were exhibited by
 one chemokine gene, suggesting that remaining diversity may hold adaptive
 potential. The low functional diversity may leave devils highly vulnerable
 to infectious disease, and therefore, monitoring and preserving remaining
 diversity will be critical for the long-term management of this species.
 Examining genetic variation in diverse immune genes should be a priority
 for threatened wildlife species. This study can act as a model for
 broad-scale immunogenetic diversity analysis in threatened species.
description: Tasmanian devil SNP
 genotypesSNP genotyping data for
 all animalsDEVILgenotypes.xlsxDevil SNPsFull devil SNP dataset for PLINKDevilGenotypes.tped.xlsxDevil TFAM fileTFAM file with individual devil details for PLINKDevilGenotypes.tfam.xlsxDevil Reads Part 01Devil Miseq reads in fastq format. Part 1.DevilReads.part01.rarDevil Reads Part 02Devil MiSeq reads in fastq format. Part 2.DevilReads.part02.rarDevil Reads Part 03Devil MiSeq reads in fastq format. Part 3.DevilReads.part03.rarDevil Reads Part 04Devil MiSeq reads in fastq format. Part 4.DevilReads.part04.rarDevil Reads Part 06Devil MiSeq reads in fastq format. Part 6.DevilReads.part06.rarDevil Reads Part 05Devil MiSeq reads in fastq format. Part 5.DevilReads.part05.rarDevil Reads Part 07Devil MiSeq reads in fastq format. Part 7.DevilReads.part07.rarDevil Reads Part 08Devil MiSeq reads in fastq format. Part 8.DevilReads.part08.rarDevil Reads Part 09Devil MiSeq reads in fastq format. Part 9.DevilReads.part09.rarDevil Reads Part 10Devil MiSeq reads in fastq format. Part 10.DevilReads.part10.rar