Data from: Cytonuclear discordance among the Southeast Asian Black rats (Rattus rattus complex)

Black rats are major invasive vertebrate pests 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. This species
complex is native to India and Southeast Asia. According to current
taxonomic classification, there are three taxa living in sympatry in
several parts of Thailand, Cambodia and Lao People's Democratic
Republic, where this study was conducted: two accepted species (Rattus
tanezumi, Rattus sakeratensis) and an additional mitochondrial lineage of
unclear taxonomic status referred to here as ‘Rattus R3’. We used
extensive sampling, morphological data and diverse genetic markers
differing in rates of evolution and parental inheritance (two
mitochondrial DNA genes, one nuclear gene and eight microsatellite loci)
to assess the reproductive isolation of these three taxa. Two close Asian
relatives, Rattus argentiventer and Rattus exulans, were also included in
the genetic analyses. Genetic analyses revealed discordance between the
mitochondrial and nuclear data. Mitochondrial phylogeny studies identified
three reciprocally monophyletic clades in the black rat complex. However,
studies of the phylogeny of the nuclear exon interphotoreceptor
retinoid-binding protein gene and clustering and assignation analyses with
eight microsatellites failed to separate R. tanezumi and R3. Morphometric
analyses were consistent with nuclear data. The incongruence between
mitochondrial and nuclear (and morphological) data rendered R. tanezumi/R3
paraphyletic for mitochondrial lineages with respect to R. sakeratensis.
Various evolutionary processes, such as shared ancestral polymorphism and
incomplete lineage sorting or hybridization with massive mitochondrial
introgression between species, may account for this unusual genetic
pattern in mammals.