Total gDNA was extracted from chimpanzee, gorilla, and human pubic lice using the Zymo Genomic DNA-Tissue MicroPrep kit following the manufacturer’s instructions except that lice were manually macerated prior to incubation with proteinase-K. Total gDNA from red colobus monkey lice was extracted using a phenol–chloroform method following Boyd et al. (2014) . DNA extracts from the Netherlands human head lice were provided by Ascunce (see Ascunce et al. 2013 (link) for collection methods).
gDNA from each louse was sonicated using the Covaris M220 instrument to an average fragment size of 300–450 bp (actual range was 200–600 bp). The sheared gDNA was prepared for next-generation sequencing using TruSeq DNAseq or Kapa Library preparation kits. The resulting library was sequenced on one-half lane of Illumina HiSeq2000 or 2500 using the TruSeq SBS sequencing kit v.1-2 for 161 cycles. All samples were sequenced paired-end, with 100 or 160 bp reads. Fastq files were produced using Casava v.1.8.2. Sequence data for the Uganda chimpanzee louse were obtained from the Genbank Short Read Archive (accession SRX390495; see Boyd et al. 2014 and Johnson et al. 2014 (link) for complete sequencing methods).
gDNA from each louse was sonicated using the Covaris M220 instrument to an average fragment size of 300–450 bp (actual range was 200–600 bp). The sheared gDNA was prepared for next-generation sequencing using TruSeq DNAseq or Kapa Library preparation kits. The resulting library was sequenced on one-half lane of Illumina HiSeq2000 or 2500 using the TruSeq SBS sequencing kit v.1-2 for 161 cycles. All samples were sequenced paired-end, with 100 or 160 bp reads. Fastq files were produced using Casava v.1.8.2. Sequence data for the Uganda chimpanzee louse were obtained from the Genbank Short Read Archive (accession SRX390495; see Boyd et al. 2014 and Johnson et al. 2014 (link) for complete sequencing methods).