Genetic rescue of the Southern Brush-tailed Rock Wallaby: is there genomic evidence it is reducing inbreeding?

Ignition Grant Round 9 (September 2018)

  • Prof Janine Deakin, UC
  • Dr Jennifer Pierson, Tidbinbilla
  • Richard Hill, VIC Department of Land, Water and Parks

The Southern Brush-tailed Rock-Wallaby is a critically endangered lineage of a species threatened across its range.  A captive breeding program was initiated in 1996 but included only 3 somewhat related founders, which resulted in low genetic diversity. In 2013, a review of the Southern Brush-tailed Rock-Wallaby (SBTRW) recovery program identified increasing genetic diversity in the captive program as the primary goal over the next five years.  The quality of the animals was identified as contributing to the lack of success in recent reintroductions and minor to major health issues have been identified in the captive population. 

To increase genetic diversity, a two-prong approach was taken by the SBTRW Recovery Team’s captive program. First, several animals from a small remnant wild population (<100 animals) were translocated from the wild to Tidbinbilla Nature Reserve. Although these are part of the breeding program, inbreeding depression has been observed in this wild population. As a result, genetic rescue of the Southern lineage was recommended (Weeks 2015) by mixing in genes from another lineage: the Central lineage. An ideal goal for this was 75 Southern/25 central and a minimum of 50/50 lineages. Additionally, a decision was made to move away from intensive management towards a more natural free-range approach to breeding that would allow a larger insurance population to be built. The aim of this insurance population is to conserve the remaining genetic diversity while providing surplus individuals for reintroductions. Two insurance populations of >100 animals will be built prior to further reintroductions. 

Tidbinbilla Nature Reserve is one of the primary institutions in the SBTRW captive program. It has been introducing Central lineage genes into the SBTRW breeding program for four years and has tissue samples available for several individuals from both the pure Southern and Central parents and F1 and F2 hybrid offspring. In addition, minor and major health issues such as heart murmurs and skin conditions have been tracked in individuals over time. Currently a microsatellite panel is used to assess the population (Weeks, cesar ltd). However, genetic diversity is so low that the data has not been very informative to management. 

The aim of this project is to develop a SNP panel that will allow the captive breeding program to evaluate the effectiveness of the genetic rescue at the genomic level. The SNP panel will be developed using DArTSeq and markers mapped to the BTRW genome (sequenced as part of the Oz Mammals Genomics initiative) which will allow the estimation of inbreeding coefficients based on runs of homozygosity (FROH). 

If the genetic rescue is effective, we would predict a reduction in FROHin F1 and F2s.  Furthermore, this panel will allow future research that evaluates inbreeding depression through phenotype-genotype relationships including evaluating general heterozygosity fitness correlations and the correlation between FROHand deleterious health effects such as heart murmurs. Finally, this panel will allow a practical and informative approach to genetic monitoring of the future captive program that is standardized across institutions. 

This project has direct and immediate policy and management applications for threatened species, conservation planning, and climate change and adaptation. This project will allow evaluation of the current Recovery Team’s policy on a Threatened Species and depending on the result, an adaptive management approach to captive breeding will applied. This project will also facilitate genetic monitoring of the captive breeding program in an informative manner that will contribute to adaptive management decision-making. 

For future conservation planning, this project can help inform the importance of lineage boundaries for this species that is threatened across it’s range by providing baseline data to evaluate inbreeding depression and outbreeding depression risks.  Finally, the genetic monitoring and adaptive genetic management of the program will allow the program to ensure that the captive program is providing maximal genetic diversity for reintroduction programs which will buffer populations from threats such as climate change and improve chances of adaptation in the face of persistent threats.