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Figure S1. The detailed phylogenetic tree from all house mouse control region sequences after Bayesian analysis, as summarised in Fig. 2 in the paper. All posterior probabilities of 0.50 and above are shown. All sequences described here from Britain, France and Ireland are highlighted. Code indicates GenBank number or code used in the publication where the sequence was first reported (Nachman et al. 1994; Gündüz et al. 2000, 2001, 2005; Hauffe et al., 2004; Rajabi-Maham et al. 2008; Förster et al. 2009; Searle et al. 2009a,b), followed by a list of the countries where the haplotype has been recorded abbreviated as here: AR, Argentina; BG, Bulgaria; CH, Switzerland; CM, Cameroon; CY, Cyprus; DE, Germany; DK, Denmark; EG, Egypt; ES, Spain; FI, Finland: FR, France; GB, Great Britain; GE, Georgia; GR, Greece; HR, Croatia; IE, Ireland; IL, Israel; IR, Iran; IT, Italy; LU, Luxembourg; MA, Morocco; MR, Mauritania; NE, Niger; NO, Norway; NZ, New Zealand; PE, Peru; PT, Portugal; SE, Sweden; TR, Turkey; US, United States.

Table S1. Details of 36 western house mouse (Mus musculus domesticus) mtDNA control region sequences included in this study in addition to the primary sequences from Britain, France and Ireland.

Table S2. Names previously given to mtDNA control region clades in the house mouse literature, and their equivalents in the currently proposed nomenclature (not all previously published clade names feature here as not all the clades are exactly equivalent to those described in this paper).

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