Supplemental data for: Ancient Genomes Reveal Over Two Thousand Years Of Dingo Population Structure

Genotype and phylogenetic analysis files for Souilmi et al. (2024). Ancient genomes reveal over two thousand years of dingo population structure. Proceedings of the National Academies of Sciences, doi: 10.1073/pnas.2407584121.

Ancient DNA genome-wide data from nine ancient dingo specimens ranging in age from 400 to 2,746 years old and 42 mitochondrial genomes pre-dating European colonists' introduction of domestic dogs to Australia.

1. Autosomal genotype files for dingo samples: We include pseudo-diploid and diploid calls for samples introduced in this study. In addition, we include genotypes for dog and Canid ancient samples from Bergstrom et al. 2020, Bergstrom et al. 2022, as well as modern Canids and dogs from Plassai et al. 2019, and Zhang et al. 2020. The genotype data are in binary plink format (.bed, .bim, .fam), and includes genotypes at polymorphic transversion sites in Californian Coyote.
2. 1. souilmi2024_bergstrom2022_bergstrom2020_zhang2020_plassais2019_finalset.bergsgrom2022-analyses-loci.tv.c2.bed: Genotype matrix.
   2. souilmi2024_bergstrom2022_bergstrom2020_zhang2020_plassais2019_finalset.bergsgrom2022-analyses-loci.tv.c2.bim: Variants chromosome, location and alleles.
   3. souilmi2024_bergstrom2022_bergstrom2020_zhang2020_plassais2019_finalset.bergsgrom2022-analyses-loci.tv.c2.fam: Sample names and population assignment (if any).
3. Mitogenomes phylogenetic analysis files:
4. 1. Mitogenomes alignment file in NEXUS format: Dingo_mtDNA.nex
   2. BEAST configuration XML file: Dingo_mtDNA.xml