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

[https://doi.org/10.5061/dryad.0k6djhbcm](https://doi.org/10.5061/dryad.0k6djhbcm)

This repository contains the data for the paper:

**\"Illuminating the mystery of thylacine extinction: a role for relaxed selection and gene loss\"**

DOI: 10.1098/rspb.2025.1339

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**Folder Structure**

* **Main folder: Thylacine_Gene_Loss.zip**
* **Chromosome_wise_Chains_and_TOGA_results:** Contains the output files of make_lastz_chains and TOGA.
* **Purpose:** Contains input, intermediate, and final output files from genome alignment and ortholog projection using LASTZ and TOGA.
* **Key Tools:**
* make_lastz_chains ([https://github.com/hillerlab/make_lastz_chains](https://github.com/hillerlab/make_lastz_chains)): pairwise genome alignment
* TOGA ([https://github.com/hillerlab/TOGA](https://github.com/hillerlab/TOGA)): identifies orthologous genes and infers gene status
* Data: 
* Chain files: pai...,