Fig. 2

Phylogenetic networks for haplogroups D and E, constructed from 772 bp of house mouse control region sequences (from positions 15,508 to 16,279 of the reference house mouse mitogenome, NC_006914). The modern sequences used to construct each network are shown in Additional File 1: Table S3. Haplogroup D network includes two of the ancient house mouse sequences (both from Battlesbury Bowl), while the haplogroup E network includes six of the ancient house mouse sequences (five Potterne and one Battlesbury Bowl). The ancient samples include OG01, 03, 09 and 10, with the asterisk in the haplogroup E network indicating OG02, 04, 07 and 08. Where there are missing data in the ancient sequences (Table 3), the sample has been placed determined on its most likely position based on the phylogenetic network. The precise position of OG10 within the D/D1 clade in the phylogenetic network may be unreliable due to missing data. Circles represent sequence haplotypes, the area being proportional to the frequency, and they are coloured by the location of the samples, as seen in the accompanying key. Small grey points are reconstructed intermediate nodes introduced by the network algorithm, and links between haplotypes represent mutations. R denotes the likely position of the root of each network, as determined from the full network (not shown)