Table 1.

Samples used for sequencing. H genotype: H_c = H_cenea, H_h = H_{hippocoonides}. #Paired-end reads: number of raw Illumina reads generated for each specimen. Estimated coverage is calculated via: (number of raw reads * read length) / length of genome assembly. Read length was 125 bp. The actual coverage is expected to be lower due to not all reads passing quality control and the presence of contamination. ‘x’ in the last two columns indicates whether the specimen carried an allele with the reference orientation and the 40 kb inversion.

voucher number	geographic origin	subspecies	phenotype	H genotype	# paired-end reads	estimated coverage	reference orientation	40 kb inversion
BMNH746848	Kenya	polytrophus	hippocoonides	Hh/Hh	38039853	41	x
BMNH746826	Kenya	polytrophus	hippocoonides	Hh/Hh	55548066	60	x
BMNH847389	Kenya	polytrophus	hippocoonides	Hh/Hh	35666867	39	x
BMNH746846	South Africa	cenea	hippocoonides	Hh/Hh	40600315	44	x
BMNH746453	Kenya	polytrophus	cenea	Hc/Hh	49512794	54	x	x
BMNH746764	Kenya	polytrophus	cenea	Hc/Hh	56085254	61	x	x
Troph-c-02–46	Kenya	polytrophus	cenea	Hc/Hh	42184635	46	x	x
BMNH847353	South Africa	cenea	cenea	Hc/?	39434400	43		x
BMNH740167	Madagascar	meriones	meriones		31242775	34	x