| Summary: | Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, their evolutionary history has received little attention and there is no firm agreement on how many species should be recognized within the Black rat complex. Members of the species complex are native from India and Southeast Asia. Current taxonomy suggests that three taxa live in sympatry in several places of Thailand, Cambodia and Lao People's Democratic Republic where the present study was conducted: two accepted species (Rattus tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of unclear taxonomic status here referred as ‘Rattus R3’. We used an extensive sampling, morphological data and diverse genetic markers of different evolutionary rates and parental inheritance (two mitochondrial DNA genes, one nuclear gene and eight microsatellite loci) to assess the reproductive isolation between these three taxa. Two close Asian relatives, Rattus argentiventer and Rattus exulans, were included in the genetic analyses for comparison. Genetic analyses revealed discordant patterns between the mitochondrial and the nuclear data. The mitochondrial phylogeny identified three reciprocally monophyletic clades in the Black rat complex. Yet, the phylogeny of the nuclear exon IRBP and the clustering and assignation analyses using the eight microsatellites failed to separate tanezumi and R3. Morphometric analyses reinforced the nuclear data. The incongruence between mitochondrial data and nuclear (and morphological) data, render tanezumi/R3 paraphyletic for mitochondrial lineages with respect to sakeratensis. Different evolutionary processes such as shared ancestral polymorphism and incomplete lineage sorting or hybridization with massive mitochondrial introgression between incipient species may be invoked to account for this unusual genetic pattern in mammals.
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