PMC:4570283 / 8424-9550 JSONTXT

{"project":"2_test","denotations":[{"id":"25937445-19779445-2051087","span":{"begin":113,"end":115},"obj":"19779445"},{"id":"25937445-24256729-2051088","span":{"begin":714,"end":716},"obj":"24256729"},{"id":"25937445-24463515-2051089","span":{"begin":779,"end":781},"obj":"24463515"},{"id":"25937445-22426219-2051090","span":{"begin":859,"end":861},"obj":"22426219"},{"id":"25937445-20644199-2051091","span":{"begin":1044,"end":1046},"obj":"20644199"},{"id":"25937445-21653522-2051092","span":{"begin":1124,"end":1126},"obj":"21653522"}],"text":"We assessed the genetic relatedness of ancient genomes to modern populations by computing outgroup f3 statistics.20 In the absence of admixture with the outgroup, the expected value of f3 (outgroup; A, B) is a function of the shared genetic history of A and B. We used the YRI as an outgroup to non-African populations and computed f3 statistic (YRI; ancient, X) to investigate the shared history of an ancient genome and a set of 32 worldwide populations, including the Kalash (X), and f3 statistic (YRI; Kalash, Y) to investigate the Kalash and a set of 32 worldwide populations and ancient genomes (Y). Ancient genomes used in the analysis included the Mal’ta boy (MA-1), a Paleolithic Siberian hunter-gatherer;25 La Braña 1, a Mesolithic European hunter-gatherer from Iberia;26 and Ötzi, the Tyrolean Iceman and a representative European Neolithic farmer.27 BAM files of the ancient genomes were downloaded from the respective references and managed with Picard v.1.112, and the genotypes were called with the Genome Analysis Toolkit v.3.3.28 Data on DNA polymorphisms were stored in VCF files and managed with VCFtools.29"}