Illuminating the mystery of thylacine extinction: A role for relaxed selection and gene loss

Gene loss shapes lineage-specific traits but is often overlooked in
species survival. In this study, we investigate the role of ancestral gene
loss using the extinct icon─thylacine (Thylacinus cynocephalus). While
studies of neutral genetic variation indicate a population decline before
extinction, the impact of thylacine-specific ancestral gene losses remains
unexplored. The availability of a chromosomal-level genome of the extinct
thylacine offers a unique opportunity for such comparative studies. Here,
we leverage palaeogenomic data to compare gene presence/absence patterns
between the Tasmanian devil and thylacine. We discovered ancestral
(between 13-1 Ma) loss of SAMD9L, HSD17B13, CUZD1, and VWA7 due to
multiple gene-inactivating mutations, corroborated by short-read
sequencing. The timing of gene loss mirrors the thylacine’s shift toward
hypercarnivory and increased body size. Notably, the loss of SAMD9
correlates with a carnivorous diet. Our genome-wide analysis reveals
olfactory receptor loss and relaxed selection, aligning with reduced
olfactory lobes in the thylacine, indicating olfaction is not its primary
hunting sense. By integrating palaeogenomic data with comparative
genomics, our study reveals ancestral gene losses and their impact on
species survival and resilience to environmental changes. Our approach can
be extended to other extinct and endangered species, helping to identify
genetic factors for conservation efforts.