Box 1: Sequencing strategies in population genomics
Whole-genome resequencing (WGR) is one of several sequencing technologies that can be used for population genomic analysis. Currently the most common family of technologies for WGR is short-read sequencing, where reads are aligned to an already-available reference genome. The per-base pair error rate is approximately 0.31% for Illumina reads (Schirmer, D’Amore, Ijaz, Hall, & Quince, 2016). Therefore, if rare variants (those that occur in few individuals, and which differ from the reference genome) need to be identified with high accuracy, high sequence depth (i.e. , a relatively large average number of reads that cover each base pair in the genome for each individual) may be required, although this can also be achieved by sequencing large population samples at low per-individual coverage. This may often be the case when using demographic inference to estimate the timing of an invasion event (see Part 3.1). In the example below, the sequence depth at the locus highlighted in grey is 11X.