Multiple Geographic Origins of Commensalism and Complex Dispersal History of Black Rats
A) Median Joining Networks. On the left network, the observed haplotypes are identified by country of origin (country codes are: AU: Australia; BR: Brazil: FR: France; GU: Guinea; GY: Guyana; IN: India; IR: Iran; JA: Japan; MA: Madagascar; NZ: New Zealand; OM: Oman; PA: Papua New Guinea; SA: Samoa; SE: Senegal; SI: Society Islands; SO: South Africa; US: United States of America; VE: Venezuela); on the right network they are identified by haplotype number as listed in Table S2. In both networks, multiple codes or numbers within a single node signify an identical haplotype coming from more than one country or locality within a country. Haplotypes marked with an asterisk are short sequences and their position on the network was inferred from a separate network analysis that produced an otherwise identical topology; B) Pairwise mismatch analyses. Separate analyses were carried out for specimens derived from the inferred natural range of Lineage I on the Indian subcontinent (a–b) and for specimens belonging to the European Black Rat population and its global ‘ship rat’ derivatives (c–d). For each population, the mismatch distribution is compared with curves derived from coalescent simulations under contrasting models of stable (a,c) or fluctuating (b,d) populations.