DOI: 10.5061/dryad.2ngf1vhjr
title: Adaptive changes in the genomes of wild rabbits after 16 years of viral epidemics

description: Since its introduction to control overabundant alien rabbits (Oryctolagus
 cuniculus), the highly virulent Rabbit Haemorrhagic Disease Virus (RHDV)
 has caused regular annual disease outbreaks in Australian rabbit
 populations. Although initially reducing rabbit abundance by 60%,
 continent-wide, experimental evidence has since indicated increased
 genetic resistance in wild rabbits that have experienced RHDV-driven
 selection. To identify genetic adaptations, which explain the increased
 resistance to this biocontrol virus, we investigated genome-wide SNP
 (single nucleotide polymorphism) allele frequency changes in a South
 Australian rabbit population that was sampled in 1996 (pre-RHD genomes)
 and after 16 years of RHDV outbreaks. We identified several SNPs with
 changed allele frequencies within or in proximity of genes that have roles
 potentially important for increased RHD resistance. Many of the identified
 genes are known to be involved in virus infections or immunity, or had
 previously been identified as being  differentially expressed in
 healthy vs. acutely RHDV-infected rabbits. Furthermore, we show in a
 simulation study that the allele/genotype frequency changes cannot be
 explained by drift alone, and that several candidate genes had also been
 identified as being associated with surviving RHD in a different
 Australian rabbit population. Our unique dataset allowed us to identify
 candidate genes for RHDV resistance that have evolved under natural
 conditions, and over a time span that would not have been feasible to
 study in an experimental setting. Moreover, it provides a rare example of
 host genetic adaptations to virus-driven selection in response to a
 suddenly emerging infectious disease.
description: Rabbit samples had been collected in 1996 from Gum Creek sheep
 station and abutting Flinders Ranges National Park in northern South
 Australia by CSIRO, Canberra, (CSIRO ethics approval 95/96-21) as part of
 a serological study to follow the epidemiology of RHDV. Samples taken
 included liver tissue for virus-capture ELISA (N = 59) to detect early
 stages of infection as well as eye lenses and body weight for age
 estimation (Cooke et al., 2000). The tissues used here were from rabbits
 which were too young to be fatally affected during the initial outbreak
 (Robinson et al., 2002) and those which had not yet been infected. They
 are termed the ‘pre-RHDV selection’ group. In 2012,
 sixteen years after the first collection, more samples were collected by
 PIRSA, Adelaide (PIRSA ethics approval 11/09). Rabbits (N = 53) were
 collected in the same way by shooting at night with a 0.22 calibre rifle
 from a vehicle equipped with a 100 W spotlight. The location of each
 rabbit shot was recorded by GPS (Garmin 72, Schaffhausen, Switzerland) to
 nearest 10 m. A liver sample was collected from each rabbit using a
 sterile scalpel and stored in a labelled 5 ml Sarstedt vial and frozen.
 All samples were stored at -18o C. The 53 rabbits sampled in 2012
 (post-RHDV selection) had been subject to approximately 15-16 generations
 under RHDV selection as every rabbit that is recruited into the breeding
 population would have had been previously exposed to RHD, and RHDV
 outbreaks had occurred regularly every year (Mutze et al., 2015, and
 additional unpublished serological data). DNA was
 extracted using the Qiagen’s Gentra Puregene mouse tail kit (Hilden,
 Germany) according to the manufacturer’s protocol. Sixteen barcodes with a
 length of 4-9 nucleotides were designed using the GBS BARCODE GENERATOR
 (v.2.0, Deena Bioinformatics). GBS libraries were constructed using the
 restriction enzyme PstI (New England Biolabs) following a published
 protocol (Elshire et al., 2011) with the adjustment that we initially
 constructed an individual library for each rabbit (N=108). All individual
 libraries were quality controlled for fragment size distribution and
 absence of adapter dimers on an Agilent 2100 Bioanalyzer using the High
 Sensitivity Kit (Agilent, Waldbronn, Germany). We prepared seven
 sequencing libraries by always pooling 16 individual libraries at equal
 molarities. Sequencing (paired-end 100-bp reads) was conducted on an
 Illumina HiSeq2000 machine by the Beijing Genomic Institute (BGI),
 China.
description: library barcode sample population 
 FCC21WPACXX-CHKPEI13070002_L6 AACTTGCAG gc3124 1996 FCC21WPACXX-CHKPEI13070002_L6 CCAGTGCAG gc3134 1996 FCC21WPACXX-CHKPEI13070002_L6 TTGAATGCAG gc3138 1996 FCC21WPACXX-CHKPEI13070002_L6 GGTCGTGCAG gc3176 1996 FCC21WPACXX-CHKPEI13070002_L6 AATGCATGCAG gc3249 1996 FCC21WPACXX-CHKPEI13070002_L6 CCATGATGCAG gc3267 1996 FCC21WPACXX-CHKPEI13070002_L6 TTGACCATGCAG gc3290 1996 FCC21WPACXX-CHKPEI13070002_L6 TGCCACATGCAG gc3291 1996 FCC21WPACXX-CHKPEI13070002_L6 GAACAATATGCAG gc2725 1996 FCC21WPACXX-CHKPEI13070002_L6 ACCACCGTTGCAG gc2730 1996 FCC21WPACXX-CHKPEI13070002_L6 CTTGTTACATGCAG gc2731 1996 FCC21WPACXX-CHKPEI13070002_L6 AGGTGGCGTTGCAG gc2766 1996 FCC21WPACXX-CHKPEI13070002_L6 GAACAACATTGCAG gc2802 1996 FCC21WPACXX-CHKPEI13070002_L6 CCTACCTGATGCAG gc2808 1996 FCC21WPACXX-CHKPEI13070002_L6 TTCTTGACATGCAG gc2880 1996 FCC21WPACXX-CHKPEI13070002_L6 AGCGGTGTTTGCAG gc2940 1996 FCC21WPACXX-CHKPEI13070003_L7 AACTTGCAG gc3299 1996 FCC21WPACXX-CHKPEI13070003_L7 CCAGTGCAG gc2388 1996 FCC21WPACXX-CHKPEI13070003_L7 TTGAATGCAG gc2554 1996 FCC21WPACXX-CHKPEI13070003_L7 GGTCGTGCAG gc3167 1996 FCC21WPACXX-CHKPEI13070003_L7 AATGCATGCAG gc2691 1996 FCC21WPACXX-CHKPEI13070003_L7 CCATGATGCAG gc2695 1996 FCC21WPACXX-CHKPEI13070003_L7 TTGACCATGCAG gc2699 1996 FCC21WPACXX-CHKPEI13070003_L7 TGCCACATGCAG gc2700 1996 FCC21WPACXX-CHKPEI13070003_L7 GAACAATATGCAG gc2706 1996 FCC21WPACXX-CHKPEI13070003_L7 ACCACCGTTGCAG gc2707 1996 FCC21WPACXX-CHKPEI13070003_L7 CTTGTTACATGCAG gc2708 1996 FCC21WPACXX-CHKPEI13070003_L7 AGGTGGCGTTGCAG gc2709 1996 FCC21WPACXX-CHKPEI13070003_L7 GAACAACATTGCAG gc2710 1996 FCC21WPACXX-CHKPEI13070003_L7 CCTACCTGATGCAG gc2726 1996 FCC21WPACXX-CHKPEI13070003_L7 TTCTTGACATGCAG gc2727 1996 FCC21WPACXX-CHKPEI13070003_L7 AGCGGTGTTTGCAG gc2728 1996 FCC229TACXX-CHKPEI13070001_L3 AACTTGCAG gc2364 1996 FCC229TACXX-CHKPEI13070001_L3 CCAGTGCAG gc2377 1996 FCC229TACXX-CHKPEI13070001_L3 TTGAATGCAG gc2378 1996 FCC229TACXX-CHKPEI13070001_L3 GGTCGTGCAG gc2380 1996 FCC229TACXX-CHKPEI13070001_L3 AATGCATGCAG gc2545 1996 FCC229TACXX-CHKPEI13070001_L3 CCATGATGCAG gc2547 1996 FCC229TACXX-CHKPEI13070001_L3 TTGACCATGCAG gc2553 1996 FCC229TACXX-CHKPEI13070001_L3 TGCCACATGCAG gc2571 1996 FCC229TACXX-CHKPEI13070001_L3 GAACAATATGCAG gc2596 1996 FCC229TACXX-CHKPEI13070001_L3 ACCACCGTTGCAG gc2597 1996 FCC229TACXX-CHKPEI13070001_L3 CTTGTTACATGCAG gc2598 1996 FCC229TACXX-CHKPEI13070001_L3 AGGTGGCGTTGCAG gc2599 1996 FCC229TACXX-CHKPEI13070001_L3 GAACAACATTGCAG gc2600 1996 FCC229TACXX-CHKPEI13070001_L3 CCTACCTGATGCAG gc2602 1996 FCC229TACXX-CHKPEI13070001_L3 TTCTTGACATGCAG gc2623 1996 FCC229TACXX-CHKPEI13070001_L3 AGCGGTGTTTGCAG gc2686 1996 FCC2GPDACXX-CHKPEI13070004_L2 AACTTGCAG ora624 2012 FCC2GPDACXX-CHKPEI13070004_L2 CCAGTGCAG ora625 2012 FCC2GPDACXX-CHKPEI13070004_L2 TTGAATGCAG ora626 2012 FCC2GPDACXX-CHKPEI13070004_L2 GGTCGTGCAG ora627 2012 FCC2GPDACXX-CHKPEI13070004_L2 AATGCATGCAG ora628 2012 FCC2GPDACXX-CHKPEI13070004_L2 CCATGATGCAG ora629 2012 FCC2GPDACXX-CHKPEI13070004_L2 TTGACCATGCAG ora630 2012 FCC2GPDACXX-CHKPEI13070004_L2 TGCCACATGCAG ora631 2012 FCC2GPDACXX-CHKPEI13070004_L2 GAACAATATGCAG ora632 2012 FCC2GPDACXX-CHKPEI13070004_L2 ACCACCGTTGCAG ora633 2012 FCC2GPDACXX-CHKPEI13070004_L2 CTTGTTACATGCAG ora634 2012 FCC2GPDACXX-CHKPEI13070004_L2 AGGTGGCGTTGCAG ora635 2012 FCC2GPDACXX-CHKPEI13070004_L2 GAACAACATTGCAG ora636 2012 FCC2GPDACXX-CHKPEI13070004_L2 CCTACCTGATGCAG ora637 2012 FCC2GPDACXX-CHKPEI13070004_L2 TTCTTGACATGCAG ora638 2012 FCC2GPDACXX-CHKPEI13070004_L2 AGCGGTGTTTGCAG ora639 2012 FCC2GPDACXX-CHKPEI13070005_L3 AACTTGCAG ora640 2012 FCC2GPDACXX-CHKPEI13070005_L3 CCAGTGCAG ora641 2012 FCC2GPDACXX-CHKPEI13070005_L3 TTGAATGCAG ora642 2012 FCC2GPDACXX-CHKPEI13070005_L3 GGTCGTGCAG ora643 2012 FCC2GPDACXX-CHKPEI13070005_L3 AATGCATGCAG ora644 2012 FCC2GPDACXX-CHKPEI13070005_L3 CCATGATGCAG ora645 2012 FCC2GPDACXX-CHKPEI13070005_L3 TTGACCATGCAG ora646 2012 FCC2GPDACXX-CHKPEI13070005_L3 TGCCACATGCAG ora647 2012 FCC2GPDACXX-CHKPEI13070005_L3 GAACAATATGCAG ora648 2012 FCC2GPDACXX-CHKPEI13070005_L3 ACCACCGTTGCAG ora649 2012 FCC2GPDACXX-CHKPEI13070005_L3 CTTGTTACATGCAG ora650 2012 FCC2GPDACXX-CHKPEI13070005_L3 AGGTGGCGTTGCAG ora651 2012 FCC2GPDACXX-CHKPEI13070005_L3 GAACAACATTGCAG ora652 2012 FCC2GPDACXX-CHKPEI13070005_L3 CCTACCTGATGCAG ora653 2012 FCC2GPDACXX-CHKPEI13070005_L3 TTCTTGACATGCAG ora654 2012 FCC2GPDACXX-CHKPEI13070005_L3 AGCGGTGTTTGCAG ora655 2012 FCC2GPDACXX-CHKPEI13070006_L4 AACTTGCAG ora656 2012 FCC2GPDACXX-CHKPEI13070006_L4 CCAGTGCAG ora657 2012 FCC2GPDACXX-CHKPEI13070006_L4 TTGAATGCAG ora658 2012 FCC2GPDACXX-CHKPEI13070006_L4 GGTCGTGCAG ora659 2012 FCC2GPDACXX-CHKPEI13070006_L4 AATGCATGCAG ora660 2012 FCC2GPDACXX-CHKPEI13070006_L4 CCATGATGCAG ora661 2012 FCC2GPDACXX-CHKPEI13070006_L4 TTGACCATGCAG ora662 2012 FCC2GPDACXX-CHKPEI13070006_L4 TGCCACATGCAG ora663 2012 FCC2GPDACXX-CHKPEI13070006_L4 GAACAATATGCAG ora664 2012 FCC2GPDACXX-CHKPEI13070006_L4 ACCACCGTTGCAG ora665 2012 FCC2GPDACXX-CHKPEI13070006_L4 CTTGTTACATGCAG ora666 2012 FCC2GPDACXX-CHKPEI13070006_L4 AGGTGGCGTTGCAG ora667 2012 FCC2GPDACXX-CHKPEI13070006_L4 GAACAACATTGCAG ora668 2012 FCC2GPDACXX-CHKPEI13070006_L4 CCTACCTGATGCAG ora669 2012 FCC2GPDACXX-CHKPEI13070006_L4 TTCTTGACATGCAG ora670 2012 FCC2GPDACXX-CHKPEI13070006_L4 AGCGGTGTTTGCAG ora671 2012 FCC2GPDACXX-CHKPEI13070007_L6 AACTTGCAG ora672 2012 FCC2GPDACXX-CHKPEI13070007_L6 CCAGTGCAG ora673 2012 FCC2GPDACXX-CHKPEI13070007_L6 TTGAATGCAG oraA 2012 FCC2GPDACXX-CHKPEI13070007_L6 GGTCGTGCAG oraB 2012 FCC2GPDACXX-CHKPEI13070007_L6 AATGCATGCAG oraC 2012 FCC2GPDACXX-CHKPEI13070007_L6 CCATGATGCAG gc2761 1996 FCC2GPDACXX-CHKPEI13070007_L6 TTGACCATGCAG gc2776 1996 FCC2GPDACXX-CHKPEI13070007_L6 TGCCACATGCAG gc2794 1996 FCC2GPDACXX-CHKPEI13070007_L6 GAACAATATGCAG gc2795 1996 FCC2GPDACXX-CHKPEI13070007_L6 ACCACCGTTGCAG gc2884 1996 FCC2GPDACXX-CHKPEI13070007_L6 CTTGTTACATGCAG gc2897 1996 FCC2GPDACXX-CHKPEI13070007_L6 AGGTGGCGTTGCAG gc2899 1996 FCC2GPDACXX-CHKPEI13070007_L6 GAACAACATTGCAG gc2901 1996 FCC2GPDACXX-CHKPEI13070007_L6 CCTACCTGATGCAG gc2917 1996 FCC2GPDACXX-CHKPEI13070007_L6 TTCTTGACATGCAG gc2922 1996 FCC2GPDACXX-CHKPEI13070007_L6 AGCGGTGTTTGCAG gc2923 1996