| Summary: | Black rats are among the major invasive vertebrates with severe ecological, economic and health impacts. Remarkably, the evolutionary history of black rats has received little attention and there is no firm agreement as how many species should be recognized within the Rattus rattus complex. Members of the species complex are native from India and Southeast Asia. Current taxonomy suggests that four taxa live in sympatry in several places of Thailand and Cambodia where the present study was conducted: three accepted species (R. tanezumi, R. losea, R. argentiventer) and an additional lineage of unclear taxonomic status sometimes referred as Rattus R3. We used an extensive sampling, morphological data and diverse genetic markers of different evolutionary rates and parental inheritance (two mtDNA genes, one nuclear gene and eight microsatellite loci) to assess the genetic structure among the four taxa. Genetic analyses revealed discordant patterns between the mt and the nuclear data. The mt phylogeny identified three reciprocally monophyletic clades corresponding to the four putative taxa while the nuclear phylogeny failed to separate tanezumi and R3. Within geographic localities, microsatellites revealed free gene flow between tanezumi and R3 but no gene flow between those two taxa and losea or argentiventer. Altogether theses analyses do not support the taxon R3 as a valid species and advocate for synonymy with tanezumi. As a consequence, R. tanezumi becomes paraphyletic with respect to losea. Simulation analyses are now ongoing to determine whether a recent speciation event between tanezumi and losea, or an incomplete lineage sorting within tanezumi could explain this uncommon pattern.
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