This project combines empirical ancient DNA (aDNA) research with bioinformatics and e-infrastructure development, structured across three primary objectives: 1. Evolutionary Genomics of Homotherium: The main usage of the resources will to continue the analyses from newly sequenced genomes of Homotherium (extinct Pleistocene scimitar-toothed cats) from Eurasia and North America. By integrating these with publicly available datasets, I will reconstruct their demographic history, assess genetic diversity, and investigate the evolutionary factors surrounding their extinction. 2. GPU Acceleration of aDNA Mapping: A major computational bottleneck in aDNA processing is the highly CPU-intensive bwa aln mapping algorithm. I am requesting GPU resources in this project to test the feasibility of migrating this step to GPUs. I will test and benchmark "BARRACUDA," an existing GPU implementation of bwa aln, against the standard CPU version. Because BARRACUDA has been reported to yield different results than CPU version, I will evaluate its accuracy for short-read aDNA mapping and explore the feasibility of developing a more accurate GPU-accelerated mapping solution. 3. Deployment and Benchmarking Pipelines: I will deploy, configure, and optimize three specialized bioinformatics pipelines built at the Centre for Palaeogenetics (CPG): DNAharvester, MitoDate, and Iterative Mapping. While DNAharvester and MitoDate are already published, the Iterative Mapping pipeline is currently in active development. I will test and benchmark it using our empirical Homotherium dataset.