Comparative phylogeography of two commensal rat species (Rattus tanezumi and R. norvegicus) in China: Insights from mitochondiral DNA, microsatellite and RADseq

Rattus norvegicus and Rattus tanezumi are dominant
species of Chinese house rats, but the colonization and demographic
history of two species in China have not been thoroughly explored.
Phylogenetic analyses with mitochondrial DNA including 486 individuals
from 31 localities revealed that R. norvegicus is widely
distributed in China, R. tanezumi is mainly distributed
in southern China with currently invading northward; northeast China was
the natal region of R. norvegicus, while the spread
of R. tanezumi in China most likely started from the southeast
coast. A total of 123 individuals from 18 localities were subjected to
2b‐RAD analyses. In the neighbor‐joining tree, individuals of R.
tanezumi grouped into geographic‐specific branches, and populations from
the southeast coast were ancestral groups, which confirmed the
colonization route from the southeast coast to central and western China.
However, individuals of R. norvegicus were generally grouped into two
clusters instead of geographic‐specific branches. One cluster comprised
inland populations, and another cluster included both southeast coast and
inland populations, which indicated that the spread history of R.
norvegicus in China was complex; in addition to on‐land colonization,
shipping transportation also played a great role. ADMIXTURE and principal
component analyses provided further supports for the colonization history.
Demographic analyses revealed that climate changes at ~40,000 to
18,000 years ago and ~4000 years ago had led to population declines of
both species; the R. norvegicus declined rapidly while the
population of R. tanezumi continuously expanded since ~1500 years
ago, indicating the importance of interspecies' competition in their
population size changes. Our study provided a valuable framework for
further investigation of phylogeography of two species in China.