MULTIPLE-SEQUENCE ALIGNMENT FILES This submission contains multiple sequence alignment files used for phylogenetic reconstructions. Sequences reconstructed from sediments are denominated by the site and layer of origin. The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence. File name Description aligned_NoSediment_10hu_10anchu_10nea_3den_1sima_1chimp Comparative data only aligned_SP3609_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from El Sidron Stratum III + comparative data aligned_SP3832_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (Main) Layer 14.3 + comparative data aligned_SP3833_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (Main) Layer 17+ comparative data aligned_SP3834_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (Main) Layer 19.1 + comparative data aligned_SP3848_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Chagyrskaya Unit 6C1 + comparative data aligned_SP3854_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (East) Layer 15 + comparative data aligned_SP3860_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (East) Layer 11.4 + comparative data aligned_SP3876_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Denisova (East) Layer 14 + comparative data aligned_SP3910_deam_10hu_10anchu_10nea_3den_1sima_1chimp Sediment from Trou Al'Wesse Stratum 17b + comparative data