Fig. 2

Phylogenetic analysis of complete cytochrome b gene (A) and complete mtDNA genome (B) of the black rat from the airplane (highlighted in red) and representative sequences of black rat lineage I. In panel (A), a complete tree of lineage I sequences including the sequence of the rat from the airplane and representative sequences of lineages II – VI is shown; a sequence from Rattus losea was used as outgroup. In panel (B), complete mtDNA genomes were analyzed in parallel using Bayesian inference (MrBayes, 50 million generations) and maximum-likelihood (PhyML, 1,000 replicates). Where both methods produced congruent nodes, posterior probabilities and bootstraps were provided, i.e. 1.00/100 (as asterisk). Values above 0.8/80 are shown. Sundamys muelleri (KY117585) was used as outgroup taxon (not shown). Country codes (ISO 3166-1 alpha-3): ARE, United Arab Emirates; ARG, Argentina; AUS, Australia; BEN, Benin; BRA, Brazil; CHL, Chile; CHN, China; CRI, Costa Rica; CMR, Cameroon; COD, Congo; DNK, Denmark; ESP, Spain; FRA, France; DEU, Germany; GIN, Guinea; GLP, Guadeloupe; GUY, Guyana; HKG, Hong Kong; HUN, Hungary; IDN, Indonesia; IRN, Iran; ISL, Iceland; ITA, Italy; JPN, Japan; MDG, Madagascar; MLI, Mali; MYS, Malaysia; KNA, St. Kitts and Nevis; NER, Niger; NGA, Nigeria; NIC, Nicaragua; PNG, Papua New Guinea; PRT, Portugal; PYF, French Polynesia; REU, Réunion; SEN, Senegal; SVN, Slovenia; SWE, Sweden; USA, United States of America; VEN, Venezuela; ZAF, South Africa; nn, not known.