Inference of population size histories

We applied smc++ (v1.11.1) (33) to infer population size histories using a previous build of the genome (hg19). All individuals for a given population were included in the analysis, with the first five individuals (alphabetically by sample name) being used as “distinguished” individuals in the composite likelihood. We assumed a mutation rate of 1.25 × 10−8 per base per generation and masked out sites according to Stephan Schiffels’ mappability mask available at https://oc.gnz.mpg.de/owncloud/index.php/s/RNQAkHcNiXZz2fd. Otherwise, all default parameter settings of smc++ were used, and a generation time of 29 years (61) was used to convert generations to years.

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