Extant and extinct bilby genomes combined with indigenous knowledge improve conservation of a unique Australian marsupial

The Ninu (Greater bilby, Macrotis lagotis) is a desert-dwelling,
culturally and ecologically important marsupial. In collaboration with
Indigenous rangers and conservation managers, we generated the first Ninu
chromosome-level genome assembly (3.66 Gbp) and genome sequences for the
extinct Yallara (Lesser bilby, Macrotis leucura). We developed and tested
a scat SNP panel, based on our genomic datasets, to inform current and
future conservation actions, to undertake future ecological assessments,
and improve our understanding of Ninu genetic diversity in managed and
wild populations. We also assessed the beneficial impact of targeted
conservation actions, like translocations, in the contemporary
metapopulation (N=363 Ninu). Resequenced genomes (temperate Ninu=6;
semi-arid Ninu=6; Yallara=4) revealed two major population crashes during
global cooling events for both species and differences in Ninu genes
involved in anatomical and metabolic pathway adaptations to aridity.
Despite their 45-year long captive history, Ninu have fewer long runs of
homozygosity than other larger mammals, which may be attributable to their
boom-bust life-history. We also investigated the unique Ninu biology using
12 tissue transcriptomes revealing expression of all 115 conserved
eutherian chorioallantoic placentation genes in the uterus; an XY1Y2 sex
chromosome system generated by fusion of the X with a large telocentric
autosome; and expansions in olfactory receptor genes. Together, we
demonstrate the holistic value of genomics in improving key conservation
management actions, understanding unique biological traits, and developing
tools for Indigenous rangers to monitor remote wild populations.