On the ancestry and evolution of the extinct dire wolf

This repository contains data files and scripts used for the publication "On the ancestry and evolution of the extinct dire wolf". This includes: 2025-03-31_CDS-MSAs_HyPhy-JSONs: tarball of the multiple sequence alignment FASTAs of the coding sequences for all 80 genes under diversifying selection in the dire wolf branch as well as the HyPhy results JSON files from BUSTED, FitMG94, FEL, and MEME programs. Supplementary_Tables: A single file with all supplementary tables (as tabs) referenced in the manuscript:S1: Sequencing library statistics for all ancient samples.S2: Reference assembly accessions used in studyS3: Alignment statistics for all ancient samplesS4: Iterative mapping and polishing statistics for paleogenome reconstructionS5: Gene annotation information for paleogenome reconstructionS6: Allele sharing statistics for residual reference bias assessmentS7: Mash distance metrics for genetic distanceS8: Short read dataset accessions used in studyS9: Mitochondrial genome accessions used in studyS10: Age estimates for nodes in phylogenetic treeS11: Summary of admixture methods and modelsS12: Selection test results by geneS13: Genes with dire wolf specific substitutions