Haplogroup A00 Males

We analyzed two haplogroup A00 males who were sequenced by Karmin et al.⁴⁴ We downloaded Y chromosome BAM files of these males from the Estonian Biocenter data repository and converted the BAM files to FASTQ files using bedtools.⁴⁵ We then processed these files using the same pipeline as the 1000 Genomes Project samples. The exception is that we did not perform GC bias correction in these samples. Autosomal data are necessary for GC correction, and only Y chromosome data were available for these males.

We simulated A00 evolution using a model of haploid genetic drift. Males can be in one of two states, reference or mutated. We began with N males, all in the reference state. Each generation, we drew a number x from a binomial distribution B(N, p + m), where p = the fraction of males in the previous generation with the mutated state and m = the mutation rate per generation per individual. We then set the number of males with the mutated state in the next generation to x. We simulated 10,000 generations, corresponding to 250,000 years of history given a generation time of 25 years. Simulations over 8,000 generations yielded similar results (data not shown).