Abstract
Historical hunting pressures on koalas in the southern part of their range in Australia have led to a marked genetic bottleneck when compared with their northern counterparts. There are a range of suspected genetic disorders such as testicular abnormalities, oxalate nephrosis and microcephaly reported at higher prevalence in these genetically restricted southern animals. This paper reports analysis of differential expression of genes from RNAseq of lymph nodes, SNPs present in genes and the fixation index (population differentiation due to genetic structure) of these SNPs from two populations, one in south east Queensland, representative of the northern genotype and one in the Mount Lofty Ranges South Australia, representative of the southern genotype. SNPs that differ between these two populations were significantly enriched in genes associated with brain diseases. Genes which were differentially expressed between the two populations included many associated with brain development or disease, and in addition a number associated with testicular development, including the androgen receptor. Finally, one of the 8 genes both differentially expressed and with a statistical difference in SNP frequency between populations was SLC26A6 (solute carrier family 26 member 6), an anion transporter that was upregulated in SA koalas and is associated with oxalate transport and calcium oxalate uroliths in humans. Together the differences in SNPs and gene expression described in this paper suggest an underlying genetic basis for several disorders commonly seen in southern Australian koalas, supporting the need for further research into the genetic basis of these conditions, and highlighting that genetic selection in managed populations may need to be considered in the future.
Highlights
Koalas (Phascolarctos cinereus) are an iconic Australian marsupial species listed as vulnerable on the IUCN ‘red list’ of threatened species (Woinarski and Burbidge 2016)
This paper reports a novel use of RNAseq data to identify the likely underlying genetic variation responsible for a number of suspect genetic disorders in a bottlenecked wildlife population
This paper takes a novel approach in the use of RNAseq data from two geographically distinct koala populations to examine differentially expressed genes and differentially segregated genes that are potentially linked to disease syndromes seen in the genetically restricted population
Summary
Koalas (Phascolarctos cinereus) are an iconic Australian marsupial species listed as vulnerable on the IUCN ‘red list’ of threatened species (Woinarski and Burbidge 2016). Small refuge populations were established on offshore Victorian islands and these koalas have been subsequently used to restock most of their former southern range These southern populations (Victoria and South Australia (SA)) are genetically distinct from the northern animals (Queensland (QLD) and New South Wales) (Neaves et al 2016; Ruiz-Rodriguez et al 2016). In contrast testicular aplasia was found to be absent in the outbred Pilliga ranges in New South Wales, with the rates of testicular abnormalities closely linked to the inbreeding co-efficients of the populations (Seymour et al 2001) Another suspected genetic disorder is the renal disease oxalate nephrosis, which has a very high prevalence in the Mount Lofty Ranges population in SA, with up to 32% of deaths attributed to this cause (Speight et al 2018). This paper provides the first evidence for an underlying genetic basis for several disorders affecting southern koala populations and sets the stage for more detailed studies to inform breeding, translocation and restocking decisions in this iconic vulnerable species
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