In addition, the above data and alignments for the published modern genomes, Denisova genome, Tianyuan individual and the two ancient genomes are available at
Data from the Illumina genotyping analysis generated in this study are available through GEO Series accession number GSE50727; PLINK files can be accessed from
performed the ancient extractions and library constructions on the modern and ancient samples —the latter with input from L.
performed mapping of MA-1 and AG-2 data sets with input from L.
provided super-computing resources, developed the next-generation sequencing pipeline and performed mapping and genotyping for all the modern genomes.
performed the autosomal contamination estimates, error rate estimates, D-statistics tests based on sequence reads and ngs Admix analyses.
performed biological sexing, mt DNA contamination estimates, PCA, Tree Mix, Mix Mapper, D-statistic tests based on allele frequencies, f-statistics and phenotypic analyses, and analysis of AG-2 using nucleotide misincorporation patterns under the supervision of R.
wrote the majority of the manuscript with critical input from R. Raw reads and alignments for the four modern genomes sequenced in this study are available for demographic research under data access agreement with E. provided access to the Mal’ta and Afontova Gora-2 samples, and K. (Mari and Avar individuals) provided modern DNA extracts for complete genome sequencing. (Altai individuals) provided access to modern DNA extracts for genotyping. carried out Illumina chip analysis on modern samples.